Tree is rooted. Will unroot.
No class=1 nodes (#1)
Optimizing branch lengths using M0
Starting lnL=-84339.264
Maximum likelihood: -69373.3363157552
Testing multiple branches
Testing branch 1/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114))#1,ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70855.513
Maximum likelihood: -68565.26679209291
Running H1
Starting lnL=-70595.925
Maximum likelihood: -68565.0794862806
Starting with D=0.3746116246038582
Rerunning H0, trying to reduce LR (D=0.3746116246038582)
Starting lnL=-68565.387
Maximum likelihood: -68565.3874497831
Rerunning H0, trying to reduce LR (D=0.3746116246038582)
Starting lnL=-68565.387
Maximum likelihood: -68565.3874497831
Final D=0.3746116246038582
lnL0=-68565.266792, lnL1=-68565.079486
Testing branch 2/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494))#1,((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72405.440
Maximum likelihood: -68564.02557902671
Running H1
Starting lnL=-70005.678
Maximum likelihood: -68562.80169830177
Starting with D=2.447761449875543
Rerunning H0, trying to reduce LR (D=2.447761449875543)
Starting lnL=-68564.434
Maximum likelihood: -68564.43380369658
Rerunning H0, trying to reduce LR (D=2.447761449875543)
Starting lnL=-68564.434
Maximum likelihood: -68564.43380369658
Final D=2.447761449875543
lnL0=-68564.025579, lnL1=-68562.801698
Testing branch 3/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357))#1,(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72172.662
Maximum likelihood: -68565.69046992961
Running H1
Starting lnL=-71030.069
Maximum likelihood: -68565.69031839016
Starting with D=0.00030307890847325325
Rerunning H0, trying to reduce LR (D=0.00030307890847325325)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031812095
Rerunning H1 because of negative LR (D=-5.384208634495735e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031787141
Final D=4.990724846720695e-07
lnL0=-68565.690318, lnL1=-68565.690318
Testing branch 4/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789)#1,(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71076.004
Maximum likelihood: -68561.85709426529
Running H1
Starting lnL=-72018.065
Maximum likelihood: -68559.99364087389
Starting with D=3.7269067828019615
Rerunning H0, trying to reduce LR (D=3.7269067828019615)
Starting lnL=-68562.493
Maximum likelihood: -68562.4930820786
Rerunning H0, trying to reduce LR (D=3.7269067828019615)
Starting lnL=-68562.493
Maximum likelihood: -68562.4930820786
Final D=3.7269067828019615
BEB analysis
pos	codon	aa	p
3	CGC	R	0.863
6	CGC	R	0.946
623	ATT	I	0.720
1140	ATA	I	0.995
1275	TAT	Y	0.745
lnL0=-68561.857094, lnL1=-68559.993641
Testing branch 5/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915))#1,ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70365.288
Maximum likelihood: -68563.69877284873
Running H1
Starting lnL=-71127.259
Maximum likelihood: -68563.66438208721
Starting with D=0.06878152303397655
Rerunning H0, trying to reduce LR (D=0.06878152303397655)
Starting lnL=-68564.709
Maximum likelihood: -68564.70931384005
Rerunning H0, trying to reduce LR (D=0.06878152303397655)
Starting lnL=-68564.709
Maximum likelihood: -68564.70931384005
Final D=0.06878152303397655
lnL0=-68563.698773, lnL1=-68563.664382
Testing branch 6/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124))))#1,((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-73312.982
Maximum likelihood: -68565.69032160666
Running H1
Starting lnL=-70045.801
Maximum likelihood: -68565.69036677483
Starting with D=-9.033633978106081e-05
Rerunning H1 because of negative LR (D=-9.033633978106081e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032101287
Rerunning H0, trying to reduce LR (D=1.1875818017870188e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032080278
Rerunning H1 because of negative LR (D=-4.201720003038645e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032062587
Final D=3.5381526686251163e-07
lnL0=-68565.690321, lnL1=-68565.690321
Testing branch 7/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237))#1,((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71434.664
Maximum likelihood: -68565.69033107716
Running H1
Starting lnL=-71381.104
Maximum likelihood: -68565.57098177396
Starting with D=0.238698606408434
Rerunning H0, trying to reduce LR (D=0.238698606408434)
Starting lnL=-68565.710
Maximum likelihood: -68565.71023032014
Rerunning H0, trying to reduce LR (D=0.238698606408434)
Starting lnL=-68565.710
Maximum likelihood: -68565.71023032014
Final D=0.238698606408434
lnL0=-68565.690331, lnL1=-68565.570982
Testing branch 8/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006)#1,(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71936.957
Maximum likelihood: -68561.80751325747
Running H1
Starting lnL=-70853.502
Maximum likelihood: -68561.11901570843
Starting with D=1.3769950980786234
Rerunning H0, trying to reduce LR (D=1.3769950980786234)
Starting lnL=-68562.475
Maximum likelihood: -68562.47526752113
Rerunning H0, trying to reduce LR (D=1.3769950980786234)
Starting lnL=-68562.475
Maximum likelihood: -68562.47526752113
Final D=1.3769950980786234
lnL0=-68561.807513, lnL1=-68561.119016
Testing branch 9/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)#1),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71855.152
Maximum likelihood: -68565.69031872033
Running H1
Starting lnL=-70363.288
Maximum likelihood: -68565.6903466193
Starting with D=-5.579795106314123e-05
Rerunning H1 because of negative LR (D=-5.579795106314123e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031724904
Rerunning H0, trying to reduce LR (D=2.942571882158518e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903169523
Rerunning H1 because of negative LR (D=-5.934853106737137e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031668206
Final D=5.404872354120016e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 10/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269)#1,ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71018.255
Maximum likelihood: -68565.69033721133
Running H1
Starting lnL=-71542.697
Maximum likelihood: -68565.69031720632
Starting with D=4.001002525910735e-05
Rerunning H0, trying to reduce LR (D=4.001002525910735e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031679761
Rerunning H1 because of negative LR (D=-8.174101822078228e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031679761
Final D=0
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 11/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982)#1,ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70770.918
Maximum likelihood: -68565.69031694847
Running H1
Starting lnL=-71325.131
Maximum likelihood: -68565.69033397581
Starting with D=-3.4054683055728674e-05
Rerunning H1 because of negative LR (D=-3.4054683055728674e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031684175
Final D=2.1344749256968498e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 12/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))#1),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72004.893
Maximum likelihood: -68565.4471342444
Running H1
Starting lnL=-85024.470
Maximum likelihood: -75304.88161573606
Starting with D=-13478.86896298331
Rerunning H1 because of negative LR (D=-13478.86896298331)
Starting lnL=-68565.447
Maximum likelihood: -68565.44713412109
Final D=2.466258592903614e-07
lnL0=-68565.447134, lnL1=-68565.447134
Testing branch 13/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082)#1,((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70507.228
Maximum likelihood: -68565.0466630569
Running H1
Starting lnL=-71569.829
Maximum likelihood: -68565.18258705224
Starting with D=-0.2718479906907305
Rerunning H1 because of negative LR (D=-0.2718479906907305)
Starting lnL=-68565.047
Maximum likelihood: -68565.04666290726
Final D=2.992746885865927e-07
lnL0=-68565.046663, lnL1=-68565.046663
Testing branch 14/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124))#1)),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-81674.966
Maximum likelihood: -68564.15799786327
Running H1
Starting lnL=-75003.957
Maximum likelihood: -68561.86499780425
Starting with D=4.586000118026277
Rerunning H0, trying to reduce LR (D=4.586000118026277)
Starting lnL=-68564.820
Maximum likelihood: -68564.8204600123
Rerunning H0, trying to reduce LR (D=4.586000118026277)
Starting lnL=-68564.820
Maximum likelihood: -68564.8204600123
Final D=4.586000118026277
BEB analysis
pos	codon	aa	p
918	GCT	A	0.959
1477	GCT	A	0.964
1517	AAG	K	0.962
lnL0=-68564.157998, lnL1=-68561.864998
Testing branch 15/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717)#1,(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71256.057
Maximum likelihood: -68565.69032157521
Running H1
Starting lnL=-71412.855
Maximum likelihood: -68565.69031852402
Starting with D=6.102374754846096e-06
Rerunning H0, trying to reduce LR (D=6.102374754846096e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031796246
Rerunning H1 because of negative LR (D=-1.1231168173253536e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031740274
Rerunning H0, trying to reduce LR (D=1.1194497346878052e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031738343
Rerunning H1 because of negative LR (D=-3.8620783016085625e-08)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031738343
Final D=0
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 16/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)#1))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71365.602
Maximum likelihood: -68563.87224814449
Running H1
Starting lnL=-70981.412
Maximum likelihood: -68563.40640501873
Starting with D=0.9316862515115645
Rerunning H0, trying to reduce LR (D=0.9316862515115645)
Starting lnL=-68564.156
Maximum likelihood: -68564.15648751322
Rerunning H0, trying to reduce LR (D=0.9316862515115645)
Starting lnL=-68564.156
Maximum likelihood: -68564.15648751322
Final D=0.9316862515115645
lnL0=-68563.872248, lnL1=-68563.406405
Testing branch 17/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)#1),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70896.027
Maximum likelihood: -68562.13268087893
Running H1
Starting lnL=-71156.261
Maximum likelihood: -68559.1967296804
Starting with D=5.871902397047961
Rerunning H0, trying to reduce LR (D=5.871902397047961)
Starting lnL=-68563.088
Maximum likelihood: -68563.08814815432
Rerunning H0, trying to reduce LR (D=5.871902397047961)
Starting lnL=-68563.088
Maximum likelihood: -68563.08814815432
Final D=5.871902397047961
BEB analysis
pos	codon	aa	p
55	GGA	G	0.946
613	GTA	V	0.995
722	GTT	V	0.691
779	ACG	T	0.986
794	GTC	V	0.645
1060	AAA	K	0.683
1182	TTT	F	0.725
1276	GTT	V	0.697
1337	GTC	V	0.606
lnL0=-68562.132681, lnL1=-68559.196730
Testing branch 18/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322)#1,ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71366.678
Maximum likelihood: -68565.65613321682
Running H1
Starting lnL=-71381.624
Maximum likelihood: -68565.67897268115
Starting with D=-0.04567892866907641
Rerunning H1 because of negative LR (D=-0.04567892866907641)
Starting lnL=-68565.656
Maximum likelihood: -68565.65613298063
Final D=4.7238427214324474e-07
lnL0=-68565.656133, lnL1=-68565.656133
Testing branch 19/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472)#1,ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72024.503
Maximum likelihood: -68565.40186603693
Running H1
Starting lnL=-70384.798
Maximum likelihood: -68564.75833669287
Starting with D=1.2870586881181225
Rerunning H0, trying to reduce LR (D=1.2870586881181225)
Starting lnL=-68565.441
Maximum likelihood: -68565.44114471812
Rerunning H0, trying to reduce LR (D=1.2870586881181225)
Starting lnL=-68565.441
Maximum likelihood: -68565.44114471812
Final D=1.2870586881181225
lnL0=-68565.401866, lnL1=-68564.758337
Testing branch 20/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191)#1,ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-69943.638
Maximum likelihood: -68565.69033848692
Running H1
Starting lnL=-70927.783
Maximum likelihood: -68565.69031796076
Starting with D=4.1052320739254355e-05
Rerunning H0, trying to reduce LR (D=4.1052320739254355e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031785616
Rerunning H1 because of negative LR (D=-2.0919833332300186e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903175655
Final D=5.81319909542799e-07
lnL0=-68565.690318, lnL1=-68565.690318
Testing branch 21/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)#1),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71770.198
Maximum likelihood: -68562.81214824923
Running H1
Starting lnL=-71619.270
Maximum likelihood: -68562.86082543238
Starting with D=-0.09735436629853211
Rerunning H1 because of negative LR (D=-0.09735436629853211)
Starting lnL=-68562.812
Maximum likelihood: -68562.8053805128
Rerunning H0, trying to reduce LR (D=0.013535472855437547)
Starting lnL=-68562.806
Maximum likelihood: -68562.8057205592
Rerunning H0, trying to reduce LR (D=0.0006800928094889969)
Starting lnL=-68562.806
Maximum likelihood: -68562.80572071373
Final D=0.0006800928094889969
lnL0=-68562.805721, lnL1=-68562.805381
Testing branch 22/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789)#1,ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71181.309
Maximum likelihood: -68565.69032085626
Running H1
Starting lnL=-71958.436
Maximum likelihood: -68565.69031779886
Starting with D=6.114802090451121e-06
Rerunning H0, trying to reduce LR (D=6.114802090451121e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031601094
Rerunning H1 because of negative LR (D=-3.5758421290665865e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031592697
Final D=1.6792910173535347e-07
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 23/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668)#1,ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70453.938
Maximum likelihood: -68564.5239474071
Running H1
Starting lnL=-73014.208
Maximum likelihood: -68564.54577507146
Starting with D=-0.0436553287145216
Rerunning H1 because of negative LR (D=-0.0436553287145216)
Starting lnL=-68564.524
Maximum likelihood: -68564.5239363089
Rerunning H0, trying to reduce LR (D=2.219638554379344e-05)
Starting lnL=-68564.524
Maximum likelihood: -68564.52393235831
Rerunning H1 because of negative LR (D=-7.901195203885436e-06)
Starting lnL=-68564.524
Maximum likelihood: -68564.5239323335
Final D=4.9622030928730965e-08
lnL0=-68564.523932, lnL1=-68564.523932
Testing branch 24/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)#1),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71651.418
Maximum likelihood: -68565.19555010404
Running H1
Starting lnL=-70992.048
Maximum likelihood: -68563.83945380339
Starting with D=2.712192601291463
Rerunning H0, trying to reduce LR (D=2.712192601291463)
Starting lnL=-68565.244
Maximum likelihood: -68565.24414420189
Rerunning H0, trying to reduce LR (D=2.712192601291463)
Starting lnL=-68565.244
Maximum likelihood: -68565.24414420189
Final D=2.712192601291463
BEB analysis
pos	codon	aa	p
74	AAA	K	0.745
771	GAG	E	0.600
1139	AGA	R	0.633
lnL0=-68565.195550, lnL1=-68563.839454
Testing branch 25/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730)#1,ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71390.146
Maximum likelihood: -68565.41361184327
Running H1
Starting lnL=-71009.280
Maximum likelihood: -68565.33560985354
Starting with D=0.15600397944217548
Rerunning H0, trying to reduce LR (D=0.15600397944217548)
Starting lnL=-68565.499
Maximum likelihood: -68565.4991233387
Rerunning H0, trying to reduce LR (D=0.15600397944217548)
Starting lnL=-68565.499
Maximum likelihood: -68565.4991233387
Final D=0.15600397944217548
lnL0=-68565.413612, lnL1=-68565.335610
Testing branch 26/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833)#1,ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71736.861
Maximum likelihood: -68565.10212631308
Running H1
Starting lnL=-71617.260
Maximum likelihood: -68565.05358138528
Starting with D=0.09708985561155714
Rerunning H0, trying to reduce LR (D=0.09708985561155714)
Starting lnL=-68565.223
Maximum likelihood: -68565.22328049353
Rerunning H0, trying to reduce LR (D=0.09708985561155714)
Starting lnL=-68565.223
Maximum likelihood: -68565.22328049353
Final D=0.09708985561155714
lnL0=-68565.102126, lnL1=-68565.053581
Testing branch 27/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)#1),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71630.600
Maximum likelihood: -68564.78008106224
Running H1
Starting lnL=-71175.677
Maximum likelihood: -68562.93932481692
Starting with D=3.68151249064249
Rerunning H0, trying to reduce LR (D=3.68151249064249)
Starting lnL=-68564.842
Maximum likelihood: -68564.84205315665
Rerunning H0, trying to reduce LR (D=3.68151249064249)
Starting lnL=-68564.842
Maximum likelihood: -68564.84205315665
Final D=3.68151249064249
BEB analysis
pos	codon	aa	p
44	GAG	E	0.832
977	CCT	P	0.986
1309	GCA	A	0.977
lnL0=-68564.780081, lnL1=-68562.939325
Testing branch 28/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499)#1,ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70129.596
Maximum likelihood: -68565.42743580995
Running H1
Starting lnL=-71419.849
Maximum likelihood: -68565.10732447977
Starting with D=0.6402226603531744
Rerunning H0, trying to reduce LR (D=0.6402226603531744)
Starting lnL=-68565.432
Maximum likelihood: -68565.43167260438
Rerunning H0, trying to reduce LR (D=0.6402226603531744)
Starting lnL=-68565.432
Maximum likelihood: -68565.43167260438
Final D=0.6402226603531744
lnL0=-68565.427436, lnL1=-68565.107324
Testing branch 29/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659)#1,ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71991.439
Maximum likelihood: -68565.1810600319
Running H1
Starting lnL=-71290.892
Maximum likelihood: -68563.97260914015
Starting with D=2.416901783493813
Rerunning H0, trying to reduce LR (D=2.416901783493813)
Starting lnL=-68565.183
Maximum likelihood: -68565.18279096452
Rerunning H0, trying to reduce LR (D=2.416901783493813)
Starting lnL=-68565.183
Maximum likelihood: -68565.18279096452
Final D=2.416901783493813
lnL0=-68565.181060, lnL1=-68563.972609
Testing branch 30/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483)#1,ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70962.774
Maximum likelihood: -68565.12780222869
Running H1
Starting lnL=-72536.731
Maximum likelihood: -68565.30665306671
Starting with D=-0.3577016760536935
Rerunning H1 because of negative LR (D=-0.3577016760536935)
Starting lnL=-68565.128
Maximum likelihood: -68565.12780221437
Final D=2.8638169169425964e-08
lnL0=-68565.127802, lnL1=-68565.127802
Testing branch 31/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153)))))#1,ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-69981.710
Maximum likelihood: -68565.690343334
Running H1
Starting lnL=-71150.037
Maximum likelihood: -68565.690332161
Starting with D=2.2346008336171508e-05
Rerunning H0, trying to reduce LR (D=2.2346008336171508e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032192715
Rerunning H1 because of negative LR (D=-2.0467705326154828e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032170493
Final D=4.444445949047804e-07
lnL0=-68565.690322, lnL1=-68565.690322
Testing branch 32/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671))))#1,((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71757.106
Maximum likelihood: -68565.67524265847
Running H1
Starting lnL=-70894.843
Maximum likelihood: -68565.68848370701
Starting with D=-0.026482097076950595
Rerunning H1 because of negative LR (D=-0.026482097076950595)
Starting lnL=-68565.675
Maximum likelihood: -68565.67524254431
Final D=2.283195499330759e-07
lnL0=-68565.675243, lnL1=-68565.675243
Testing branch 33/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148)))#1,(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71229.738
Maximum likelihood: -68565.69032084076
Running H1
Starting lnL=-75943.678
Maximum likelihood: -68565.69032093884
Starting with D=-1.9615981727838516e-07
Rerunning H1 because of negative LR (D=-1.9615981727838516e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032043082
Final D=8.198840077966452e-07
lnL0=-68565.690321, lnL1=-68565.690320
Testing branch 34/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410)#1,((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71225.989
Maximum likelihood: -68563.44543472657
Running H1
Starting lnL=-73447.476
Maximum likelihood: -68562.91447485988
Starting with D=1.0619197333871853
Rerunning H0, trying to reduce LR (D=1.0619197333871853)
Starting lnL=-68564.223
Maximum likelihood: -68564.22274316639
Rerunning H0, trying to reduce LR (D=1.0619197333871853)
Starting lnL=-68564.223
Maximum likelihood: -68564.22274316639
Final D=1.0619197333871853
lnL0=-68563.445435, lnL1=-68562.914475
Testing branch 35/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595)#1,ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71652.435
Maximum likelihood: -68565.69032646967
Running H1
Starting lnL=-71127.964
Maximum likelihood: -68565.69036010282
Starting with D=-6.726628635078669e-05
Rerunning H1 because of negative LR (D=-6.726628635078669e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903263814
Final D=1.7654383555054665e-07
lnL0=-68565.690326, lnL1=-68565.690326
Testing branch 36/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544)#1,ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70832.058
Maximum likelihood: -68565.69031665547
Running H1
Starting lnL=-69929.094
Maximum likelihood: -68565.69032803763
Starting with D=-2.276431769132614e-05
Rerunning H1 because of negative LR (D=-2.276431769132614e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031665547
Final D=0
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 37/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))#1),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71584.006
Maximum likelihood: -68564.49703951848
Running H1
Starting lnL=-72061.989
Maximum likelihood: -68561.36295070207
Starting with D=6.268177632824518
Rerunning H0, trying to reduce LR (D=6.268177632824518)
Starting lnL=-68565.211
Maximum likelihood: -68565.21080913368
Rerunning H0, trying to reduce LR (D=6.268177632824518)
Starting lnL=-68565.211
Maximum likelihood: -68565.21080913368
Final D=6.268177632824518
BEB analysis
pos	codon	aa	p
1128	GCA	A	0.971
1364	GCA	A	0.932
lnL0=-68564.497040, lnL1=-68561.362951
Testing branch 38/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358))#1,(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71496.105
Maximum likelihood: -68565.69040083927
Running H1
Starting lnL=-74541.081
Maximum likelihood: -68565.6903549739
Starting with D=9.173073340207338e-05
Rerunning H0, trying to reduce LR (D=9.173073340207338e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903549739
Final D=0
lnL0=-68565.690355, lnL1=-68565.690355
Testing branch 39/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192))#1,(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70903.180
Maximum likelihood: -68565.66023617674
Running H1
Starting lnL=-71759.603
Maximum likelihood: -68565.68959445336
Starting with D=-0.05871655323426239
Rerunning H1 because of negative LR (D=-0.05871655323426239)
Starting lnL=-68565.660
Maximum likelihood: -68565.66023002443
Rerunning H0, trying to reduce LR (D=1.2304633855819702e-05)
Starting lnL=-68565.660
Maximum likelihood: -68565.66022926912
Rerunning H1 because of negative LR (D=-1.5106052160263062e-06)
Starting lnL=-68565.660
Maximum likelihood: -68565.66022898864
Final D=5.609763320535421e-07
lnL0=-68565.660229, lnL1=-68565.660229
Testing branch 40/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059)#1,((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71933.534
Maximum likelihood: -68565.61752879682
Running H1
Starting lnL=-70808.276
Maximum likelihood: -68565.66104300499
Starting with D=-0.08702841633930802
Rerunning H1 because of negative LR (D=-0.08702841633930802)
Starting lnL=-68565.618
Maximum likelihood: -68565.61752743002
Rerunning H0, trying to reduce LR (D=2.73360637947917e-06)
Starting lnL=-68565.618
Maximum likelihood: -68565.6175274051
Rerunning H1 because of negative LR (D=-4.98257577419281e-08)
Starting lnL=-68565.618
Maximum likelihood: -68565.6175273863
Final D=3.7602148950099945e-08
lnL0=-68565.617527, lnL1=-68565.617527
Testing branch 41/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799)#1,ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70143.000
Maximum likelihood: -68564.45141820832
Running H1
Starting lnL=-70571.103
Maximum likelihood: -68564.11372211043
Starting with D=0.6753921957861166
Rerunning H0, trying to reduce LR (D=0.6753921957861166)
Starting lnL=-68564.349
Maximum likelihood: -68564.34871728011
Rerunning H0, trying to reduce LR (D=0.46999033936299384)
Starting lnL=-68564.349
Maximum likelihood: -68564.3487459196
Final D=0.46999033936299384
lnL0=-68564.348717, lnL1=-68564.113722
Testing branch 42/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821)#1,ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70600.266
Maximum likelihood: -68565.63526461886
Running H1
Starting lnL=-71273.077
Maximum likelihood: -68565.64755582434
Starting with D=-0.024582410958828405
Rerunning H1 because of negative LR (D=-0.024582410958828405)
Starting lnL=-68565.635
Maximum likelihood: -68565.63526421458
Final D=8.085626177489758e-07
lnL0=-68565.635265, lnL1=-68565.635264
Testing branch 43/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)#1),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70848.381
Maximum likelihood: -68565.69032339609
Running H1
Starting lnL=-71603.755
Maximum likelihood: -68565.69031717147
Starting with D=1.2449250789359212e-05
Rerunning H0, trying to reduce LR (D=1.2449250789359212e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031717147
Final D=0
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 44/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039)#1,ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71947.301
Maximum likelihood: -68563.87780288457
Running H1
Starting lnL=-71319.449
Maximum likelihood: -68564.13314559017
Starting with D=-0.5106854111945722
Rerunning H1 because of negative LR (D=-0.5106854111945722)
Starting lnL=-68563.878
Maximum likelihood: -68563.87776084496
Rerunning H0, trying to reduce LR (D=8.407921995967627e-05)
Starting lnL=-68563.878
Maximum likelihood: -68563.87776039855
Rerunning H1 because of negative LR (D=-8.928182069212198e-07)
Starting lnL=-68563.878
Maximum likelihood: -68563.87776023058
Final D=3.3594551496207714e-07
lnL0=-68563.877760, lnL1=-68563.877760
Testing branch 45/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)#1),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71026.414
Maximum likelihood: -68565.66107562676
Running H1
Starting lnL=-70033.765
Maximum likelihood: -68565.68884437179
Starting with D=-0.05553749005775899
Rerunning H1 because of negative LR (D=-0.05553749005775899)
Starting lnL=-68565.661
Maximum likelihood: -68565.661072445
Rerunning H0, trying to reduce LR (D=6.3635234255343676e-06)
Starting lnL=-68565.661
Maximum likelihood: -68565.66107209276
Rerunning H1 because of negative LR (D=-7.04487320035696e-07)
Starting lnL=-68565.661
Maximum likelihood: -68565.66107195214
Final D=2.812303137034178e-07
lnL0=-68565.661072, lnL1=-68565.661072
Testing branch 46/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135)#1,ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71618.390
Maximum likelihood: -68565.69031656494
Running H1
Starting lnL=-71646.950
Maximum likelihood: -68565.6903174067
Starting with D=-1.683511072769761e-06
Rerunning H1 because of negative LR (D=-1.683511072769761e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031646226
Final D=2.05356627702713e-07
lnL0=-68565.690317, lnL1=-68565.690316
Testing branch 47/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310)#1,ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71567.236
Maximum likelihood: -68565.69031608608
Running H1
Starting lnL=-71211.828
Maximum likelihood: -68565.69032721364
Starting with D=-2.225511707365513e-05
Rerunning H1 because of negative LR (D=-2.225511707365513e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031590127
Final D=3.6961864680051804e-07
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 48/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148)#1)),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70694.933
Maximum likelihood: -68565.69031702161
Running H1
Starting lnL=-71201.960
Maximum likelihood: -68565.6903599123
Starting with D=-8.578138658776879e-05
Rerunning H1 because of negative LR (D=-8.578138658776879e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031697574
Final D=9.173527359962463e-08
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 49/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970)#1,ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-89999.053
Maximum likelihood: -68565.69033924886
Running H1
Starting lnL=-70249.011
Maximum likelihood: -68565.69031779749
Starting with D=4.2902742279693484e-05
Rerunning H0, trying to reduce LR (D=4.2902742279693484e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031719115
Rerunning H1 because of negative LR (D=-1.2126693036407232e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903170781
Final D=2.2610765881836414e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 50/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923)#1,ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71430.472
Maximum likelihood: -68564.79809922326
Running H1
Starting lnL=-70828.993
Maximum likelihood: -68564.96725896503
Starting with D=-0.3383194835332688
Rerunning H1 because of negative LR (D=-0.3383194835332688)
Starting lnL=-68564.798
Maximum likelihood: -68564.79809656214
Rerunning H0, trying to reduce LR (D=5.322246579453349e-06)
Starting lnL=-68564.798
Maximum likelihood: -68564.79809652375
Rerunning H1 because of negative LR (D=-7.677590474486351e-08)
Starting lnL=-68564.798
Maximum likelihood: -68564.7980961147
Final D=8.181086741387844e-07
lnL0=-68564.798097, lnL1=-68564.798096
Testing branch 51/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))#1),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70403.209
Maximum likelihood: -68565.6903269352
Running H1
Starting lnL=-71093.481
Maximum likelihood: -68565.67799486131
Starting with D=0.0246641477860976
Rerunning H0, trying to reduce LR (D=0.0246641477860976)
Starting lnL=-68565.716
Maximum likelihood: -68565.7156054855
Rerunning H0, trying to reduce LR (D=0.0246641477860976)
Starting lnL=-68565.716
Maximum likelihood: -68565.7156054855
Final D=0.0246641477860976
lnL0=-68565.690327, lnL1=-68565.677995
Testing branch 52/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004))#1,((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71293.001
Maximum likelihood: -68565.69031818165
Running H1
Starting lnL=-70480.562
Maximum likelihood: -68565.69031827599
Starting with D=-1.886801328510046e-07
Rerunning H1 because of negative LR (D=-1.886801328510046e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031813888
Final D=8.553615771234035e-08
lnL0=-68565.690318, lnL1=-68565.690318
Testing branch 53/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306))#1,((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71253.346
Maximum likelihood: -68565.37208092262
Running H1
Starting lnL=-71509.454
Maximum likelihood: -68563.37729484963
Starting with D=3.989572145976126
Rerunning H0, trying to reduce LR (D=3.989572145976126)
Starting lnL=-68565.379
Maximum likelihood: -68565.37918066146
Rerunning H0, trying to reduce LR (D=3.989572145976126)
Starting lnL=-68565.379
Maximum likelihood: -68565.37918066146
Final D=3.989572145976126
BEB analysis
pos	codon	aa	p
600	GAA	E	0.711
1382	AAG	K	0.701
1504	CGT	R	0.969
lnL0=-68565.372081, lnL1=-68563.377295
Testing branch 54/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364))#1,((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70605.569
Maximum likelihood: -68565.66509113064
Running H1
Starting lnL=-76090.467
Maximum likelihood: -68565.69021183164
Starting with D=-0.05024140200112015
Rerunning H1 because of negative LR (D=-0.05024140200112015)
Starting lnL=-68565.665
Maximum likelihood: -68565.66509074908
Final D=7.631024345755577e-07
lnL0=-68565.665091, lnL1=-68565.665091
Testing branch 55/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430)#1,(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-75017.689
Maximum likelihood: -68565.6903190022
Running H1
Starting lnL=-81832.981
Maximum likelihood: -76727.5611892265
Starting with D=-16323.741740448604
Rerunning H1 because of negative LR (D=-16323.741740448604)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031788543
Rerunning H0, trying to reduce LR (D=2.2335443645715714e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031698341
Rerunning H1 because of negative LR (D=-1.8040300346910954e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031651728
Final D=9.32253897190094e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 56/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)#1),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71043.315
Maximum likelihood: -68564.38735757412
Running H1
Starting lnL=-72019.052
Maximum likelihood: -68561.20798576447
Starting with D=6.3587436192901805
Rerunning H0, trying to reduce LR (D=6.3587436192901805)
Starting lnL=-68565.292
Maximum likelihood: -68565.2920082379
Rerunning H0, trying to reduce LR (D=6.3587436192901805)
Starting lnL=-68565.292
Maximum likelihood: -68565.2920082379
Final D=6.3587436192901805
BEB analysis
pos	codon	aa	p
724	ATT	I	0.538
759	ATC	I	0.538
875	AAA	K	0.954
1316	AAG	K	0.973
lnL0=-68564.387358, lnL1=-68561.207986
Testing branch 57/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)#1),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71957.011
Maximum likelihood: -68565.6899230378
Running H1
Starting lnL=-71636.444
Maximum likelihood: -68565.67984744978
Starting with D=0.020151176053332165
Rerunning H0, trying to reduce LR (D=0.020151176053332165)
Starting lnL=-68565.691
Maximum likelihood: -68565.6908273589
Rerunning H0, trying to reduce LR (D=0.020151176053332165)
Starting lnL=-68565.691
Maximum likelihood: -68565.6908273589
Final D=0.020151176053332165
lnL0=-68565.689923, lnL1=-68565.679847
Testing branch 58/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044)#1,ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70692.965
Maximum likelihood: -68565.15069691048
Running H1
Starting lnL=-70744.238
Maximum likelihood: -68565.1687541879
Starting with D=-0.03611455482314341
Rerunning H1 because of negative LR (D=-0.03611455482314341)
Starting lnL=-68565.151
Maximum likelihood: -68565.15069691048
Final D=0
lnL0=-68565.150697, lnL1=-68565.150697
Testing branch 59/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)#1),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70400.337
Maximum likelihood: -68564.60570206435
Running H1
Starting lnL=-79213.551
Maximum likelihood: -76326.9681989496
Starting with D=-15524.724993770506
Rerunning H1 because of negative LR (D=-15524.724993770506)
Starting lnL=-68564.606
Maximum likelihood: -68561.52357277338
Rerunning H0, trying to reduce LR (D=6.164258581935428)
Starting lnL=-68565.237
Maximum likelihood: -68565.23743374404
Rerunning H0, trying to reduce LR (D=6.164258581935428)
Starting lnL=-68565.237
Maximum likelihood: -68565.23743374404
Final D=6.164258581935428
BEB analysis
pos	codon	aa	p
179	AGT	S	0.938
724	ATT	I	0.548
lnL0=-68564.605702, lnL1=-68561.523573
Testing branch 60/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531)#1,ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70617.463
Maximum likelihood: -68565.69032393527
Running H1
Starting lnL=-70744.580
Maximum likelihood: -68565.69032153608
Starting with D=4.7983776312321424e-06
Rerunning H0, trying to reduce LR (D=4.7983776312321424e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031842127
Rerunning H1 because of negative LR (D=-6.229616701602936e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031778413
Rerunning H0, trying to reduce LR (D=1.2742821127176285e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031699354
Rerunning H1 because of negative LR (D=-1.5811820048838854e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031692883
Final D=1.2942473404109478e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 61/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671))#1)),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70335.198
Maximum likelihood: -68565.24137011904
Running H1
Starting lnL=-70630.231
Maximum likelihood: -68564.98821217641
Starting with D=0.5063158852572087
Rerunning H0, trying to reduce LR (D=0.5063158852572087)
Starting lnL=-68565.378
Maximum likelihood: -68565.37752937892
Rerunning H0, trying to reduce LR (D=0.5063158852572087)
Starting lnL=-68565.378
Maximum likelihood: -68565.37752937892
Final D=0.5063158852572087
lnL0=-68565.241370, lnL1=-68564.988212
Testing branch 62/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189)#1,(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70782.885
Maximum likelihood: -68565.26469734107
Running H1
Starting lnL=-74328.409
Maximum likelihood: -68564.67908387994
Starting with D=1.1712269222771283
Rerunning H0, trying to reduce LR (D=1.1712269222771283)
Starting lnL=-68565.411
Maximum likelihood: -68565.41127553405
Rerunning H0, trying to reduce LR (D=1.1712269222771283)
Starting lnL=-68565.411
Maximum likelihood: -68565.41127553405
Final D=1.1712269222771283
lnL0=-68565.264697, lnL1=-68564.679084
Testing branch 63/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)#1))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71571.720
Maximum likelihood: -68565.6903163475
Running H1
Starting lnL=-70943.198
Maximum likelihood: -68565.69032462269
Starting with D=-1.6550358850508928e-05
Rerunning H1 because of negative LR (D=-1.6550358850508928e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031624025
Final D=2.1452433429658413e-07
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 64/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664)#1,ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71326.709
Maximum likelihood: -68565.69033258129
Running H1
Starting lnL=-71489.951
Maximum likelihood: -68565.69033609415
Starting with D=-7.0257228799164295e-06
Rerunning H1 because of negative LR (D=-7.0257228799164295e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69033164285
Rerunning H0, trying to reduce LR (D=1.8768769223242998e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69033049114
Rerunning H1 because of negative LR (D=-2.303422661498189e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032246123
Rerunning H0, trying to reduce LR (D=1.6059813788160682e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032241481
Rerunning H1 because of negative LR (D=-9.284121915698051e-08)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032219125
Final D=4.471221473067999e-07
lnL0=-68565.690322, lnL1=-68565.690322
Testing branch 65/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958))#1,ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-73593.722
Maximum likelihood: -68565.52379059368
Running H1
Starting lnL=-70941.348
Maximum likelihood: -68565.01163539874
Starting with D=1.024310389882885
Rerunning H0, trying to reduce LR (D=1.024310389882885)
Starting lnL=-68565.560
Maximum likelihood: -68565.55972967522
Rerunning H0, trying to reduce LR (D=1.024310389882885)
Starting lnL=-68565.560
Maximum likelihood: -68565.55972967522
Final D=1.024310389882885
lnL0=-68565.523791, lnL1=-68565.011635
Testing branch 66/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219)#1,(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72041.966
Maximum likelihood: -68565.6903162087
Running H1
Starting lnL=-70690.816
Maximum likelihood: -68565.69032528676
Starting with D=-1.8156133592128754e-05
Rerunning H1 because of negative LR (D=-1.8156133592128754e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031597806
Final D=4.6126660890877247e-07
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 67/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631)#1,ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72189.632
Maximum likelihood: -68565.69032264409
Running H1
Starting lnL=-70838.907
Maximum likelihood: -68565.69034186026
Starting with D=-3.8432335713878274e-05
Rerunning H1 because of negative LR (D=-3.8432335713878274e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032173588
Rerunning H0, trying to reduce LR (D=1.816428266465664e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032171147
Rerunning H1 because of negative LR (D=-4.880712367594242e-08)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032171147
Final D=0
lnL0=-68565.690322, lnL1=-68565.690322
Testing branch 68/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160)#1,ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70242.190
Maximum likelihood: -68565.69032206963
Running H1
Starting lnL=-70420.937
Maximum likelihood: -68565.69031981548
Starting with D=4.508299753069878e-06
Rerunning H0, trying to reduce LR (D=4.508299753069878e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031866391
Rerunning H1 because of negative LR (D=-2.3031316231936216e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031847709
Final D=3.736349754035473e-07
lnL0=-68565.690319, lnL1=-68565.690318
Testing branch 69/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955)#1,MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72395.532
Maximum likelihood: -68565.6903267764
Running H1
Starting lnL=-86026.940
Maximum likelihood: -68565.69031977314
Starting with D=1.4006509445607662e-05
Rerunning H0, trying to reduce LR (D=1.4006509445607662e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031963471
Rerunning H1 because of negative LR (D=-2.768647391349077e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031954405
Final D=1.8131686374545097e-07
lnL0=-68565.690320, lnL1=-68565.690320
Testing branch 70/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662)#1,MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70341.632
Maximum likelihood: -68565.69042304643
Running H1
Starting lnL=-70984.849
Maximum likelihood: -68565.69034425638
Starting with D=0.000157580099767074
Rerunning H0, trying to reduce LR (D=0.000157580099767074)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903439786
Rerunning H1 because of negative LR (D=-5.555630195885897e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.690343944
Final D=6.917980499565601e-08
lnL0=-68565.690344, lnL1=-68565.690344
Testing branch 71/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734)#1,MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70757.624
Maximum likelihood: -68565.69032827218
Running H1
Starting lnL=-71533.897
Maximum likelihood: -68565.6903161062
Starting with D=2.4331966415047646e-05
Rerunning H0, trying to reduce LR (D=2.4331966415047646e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031607313
Rerunning H1 because of negative LR (D=-6.612390279769897e-08)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031607313
Final D=0
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 72/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)#1),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70341.257
Maximum likelihood: -68565.47541510354
Running H1
Starting lnL=-70682.486
Maximum likelihood: -68565.56543806528
Starting with D=-0.18004592348006554
Rerunning H1 because of negative LR (D=-0.18004592348006554)
Starting lnL=-68565.475
Maximum likelihood: -68565.47536679765
Rerunning H0, trying to reduce LR (D=9.66117950156331e-05)
Starting lnL=-68565.475
Maximum likelihood: -68565.47536586226
Rerunning H1 because of negative LR (D=-1.8707651179283857e-06)
Starting lnL=-68565.475
Maximum likelihood: -68565.47536536427
Final D=9.959912858903408e-07
lnL0=-68565.475366, lnL1=-68565.475365
Testing branch 73/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943)#1,ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70804.271
Maximum likelihood: -68565.69032008506
Running H1
Starting lnL=-73025.519
Maximum likelihood: -68565.69033564813
Starting with D=-3.11261392198503e-05
Rerunning H1 because of negative LR (D=-3.11261392198503e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031751328
Rerunning H0, trying to reduce LR (D=5.143578164279461e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031680502
Rerunning H1 because of negative LR (D=-1.416512532159686e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031660742
Final D=3.9520091377198696e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 74/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071)#1,ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71716.942
Maximum likelihood: -68565.69032504046
Running H1
Starting lnL=-70679.130
Maximum likelihood: -68565.69032846169
Starting with D=-6.842456059530377e-06
Rerunning H1 because of negative LR (D=-6.842456059530377e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032405922
Rerunning H0, trying to reduce LR (D=1.9624712876975536e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.690323095
Rerunning H1 because of negative LR (D=-1.928448909893632e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032233173
Rerunning H0, trying to reduce LR (D=1.5265250112861395e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032097438
Rerunning H1 because of negative LR (D=-2.7147179935127497e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032013063
Rerunning H0, trying to reduce LR (D=1.6874982975423336e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031994027
Rerunning H1 because of negative LR (D=-3.807072062045336e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031994027
Final D=0
lnL0=-68565.690320, lnL1=-68565.690320
Testing branch 75/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117)#1,ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71589.175
Maximum likelihood: -68565.69031584308
Running H1
Starting lnL=-70860.720
Maximum likelihood: -68565.69032552978
Starting with D=-1.937340130098164e-05
Rerunning H1 because of negative LR (D=-1.937340130098164e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031584308
Final D=0
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 76/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881)#1,ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70806.754
Maximum likelihood: -68565.87838151837
Running H1
Starting lnL=-70868.017
Maximum likelihood: -68565.69032018642
Starting with D=0.3761226639035158
Rerunning H0, trying to reduce LR (D=0.3761226639035158)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031991687
Rerunning H1 because of negative LR (D=-5.390902515500784e-07)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031989439
Final D=4.496541805565357e-08
lnL0=-68565.690320, lnL1=-68565.690320
Testing branch 77/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))#1),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70075.454
Maximum likelihood: -68565.69046289581
Running H1
Starting lnL=-69994.568
Maximum likelihood: -68565.69032049776
Starting with D=0.0002847961150109768
Rerunning H0, trying to reduce LR (D=0.0002847961150109768)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031965107
Rerunning H1 because of negative LR (D=-1.6933772712945938e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031870445
Rerunning H0, trying to reduce LR (D=1.8932332750409842e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031813476
Rerunning H1 because of negative LR (D=-1.1393858585506678e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031778585
Final D=6.97822542861104e-07
lnL0=-68565.690318, lnL1=-68565.690318
Testing branch 78/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182)#1,(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-73645.024
Maximum likelihood: -68565.69033733143
Running H1
Starting lnL=-71956.361
Maximum likelihood: -68565.69031875905
Starting with D=3.714475315064192e-05
Rerunning H0, trying to reduce LR (D=3.714475315064192e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031806287
Rerunning H1 because of negative LR (D=-1.3923563528805971e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031786379
Final D=3.981695044785738e-07
lnL0=-68565.690318, lnL1=-68565.690318
Testing branch 79/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153)))#1)),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70931.903
Maximum likelihood: -68565.69677362795
Running H1
Starting lnL=-71397.248
Maximum likelihood: -68565.53999234433
Starting with D=0.3135625672293827
Rerunning H0, trying to reduce LR (D=0.3135625672293827)
Starting lnL=-68565.602
Maximum likelihood: -68565.5575642523
Rerunning H0, trying to reduce LR (D=0.03514381594141014)
Starting lnL=-68565.602
Maximum likelihood: -68565.60210736016
Final D=0.03514381594141014
lnL0=-68565.557564, lnL1=-68565.539992
Testing branch 80/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027)#1,((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72818.505
Maximum likelihood: -68565.55440499344
Running H1
Starting lnL=-71762.757
Maximum likelihood: -68565.31032036513
Starting with D=0.48816925662686117
Rerunning H0, trying to reduce LR (D=0.48816925662686117)
Starting lnL=-68565.571
Maximum likelihood: -68565.57063828327
Rerunning H0, trying to reduce LR (D=0.48816925662686117)
Starting lnL=-68565.571
Maximum likelihood: -68565.57063828327
Final D=0.48816925662686117
lnL0=-68565.554405, lnL1=-68565.310320
Testing branch 81/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552)#1,ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71381.885
Maximum likelihood: -68564.81216187555
Running H1
Starting lnL=-70701.369
Maximum likelihood: -68563.53978374078
Starting with D=2.5447562695480883
Rerunning H0, trying to reduce LR (D=2.5447562695480883)
Starting lnL=-68565.012
Maximum likelihood: -68565.0120382554
Rerunning H0, trying to reduce LR (D=2.5447562695480883)
Starting lnL=-68565.012
Maximum likelihood: -68565.0120382554
Final D=2.5447562695480883
lnL0=-68564.812162, lnL1=-68563.539784
Testing branch 82/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829)#1,ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71079.623
Maximum likelihood: -68565.67146116756
Running H1
Starting lnL=-69980.087
Maximum likelihood: -68565.69035223409
Starting with D=-0.03778213306213729
Rerunning H1 because of negative LR (D=-0.03778213306213729)
Starting lnL=-68565.671
Maximum likelihood: -68565.67146041783
Rerunning H0, trying to reduce LR (D=1.4994584489613771e-06)
Starting lnL=-68565.671
Maximum likelihood: -68565.67145919419
Rerunning H1 because of negative LR (D=-2.4472828954458237e-06)
Starting lnL=-68565.671
Maximum likelihood: -68565.6714586113
Rerunning H0, trying to reduce LR (D=1.1657830327749252e-06)
Starting lnL=-68565.671
Maximum likelihood: -68565.67145736008
Rerunning H1 because of negative LR (D=-2.502434654161334e-06)
Starting lnL=-68565.671
Maximum likelihood: -68565.67145686252
Final D=9.951181709766388e-07
lnL0=-68565.671457, lnL1=-68565.671457
Testing branch 83/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247)#1,ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71393.772
Maximum likelihood: -68565.4924178441
Running H1
Starting lnL=-70407.161
Maximum likelihood: -68565.52337380896
Starting with D=-0.061911929718917236
Rerunning H1 because of negative LR (D=-0.061911929718917236)
Starting lnL=-68565.492
Maximum likelihood: -68565.49238555688
Rerunning H0, trying to reduce LR (D=6.457444396801293e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49235256053
Rerunning H1 because of negative LR (D=-6.599270273000002e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49230402203
Rerunning H0, trying to reduce LR (D=9.707699064165354e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49225816195
Rerunning H1 because of negative LR (D=-9.172016871161759e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.4922173461
Rerunning H0, trying to reduce LR (D=8.163170423358679e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49217855714
Rerunning H1 because of negative LR (D=-7.757791900075972e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49214335422
Rerunning H0, trying to reduce LR (D=7.040583295747638e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49210618717
Rerunning H1 because of negative LR (D=-7.433409336954355e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49206581342
Rerunning H0, trying to reduce LR (D=8.074750076048076e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49202883919
Rerunning H1 because of negative LR (D=-7.394846761599183e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49199041408
Rerunning H0, trying to reduce LR (D=7.685020682401955e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49195068206
Rerunning H1 because of negative LR (D=-7.946405094116926e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49191846878
Rerunning H0, trying to reduce LR (D=6.442656740546227e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49189090573
Rerunning H1 because of negative LR (D=-5.512608913704753e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49185553442
Performed %!s(MISSING) optimization, finishing
Rerunning H0, trying to reduce LR (D=7.07426224835217e-05)
Starting lnL=-68565.492
Maximum likelihood: -68565.49185555172
Final D=3.4604454413056374e-08
lnL0=-68565.491856, lnL1=-68565.491856
Testing branch 84/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921)#1,ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-73332.647
Maximum likelihood: -68564.93469032152
Running H1
Starting lnL=-70973.722
Maximum likelihood: -68564.81433072922
Starting with D=0.24071918459958397
Rerunning H0, trying to reduce LR (D=0.24071918459958397)
Starting lnL=-68565.116
Maximum likelihood: -68565.11605287196
Rerunning H0, trying to reduce LR (D=0.24071918459958397)
Starting lnL=-68565.116
Maximum likelihood: -68565.11605287196
Final D=0.24071918459958397
lnL0=-68564.934690, lnL1=-68564.814331
Testing branch 85/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910)#1,ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71364.928
Maximum likelihood: -68565.69033979443
Running H1
Starting lnL=-70625.061
Maximum likelihood: -68565.6903193542
Starting with D=4.088046262040734e-05
Rerunning H0, trying to reduce LR (D=4.088046262040734e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031853815
Rerunning H1 because of negative LR (D=-1.6320846043527126e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031853815
Final D=0
lnL0=-68565.690319, lnL1=-68565.690319
Testing branch 86/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))#1))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71117.522
Maximum likelihood: -68565.69035017092
Running H1
Starting lnL=-71174.841
Maximum likelihood: -68565.69031680397
Starting with D=6.673388998024166e-05
Rerunning H0, trying to reduce LR (D=6.673388998024166e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031613834
Rerunning H1 because of negative LR (D=-1.331267412751913e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031613834
Final D=0
lnL0=-68565.690316, lnL1=-68565.690316
Testing branch 87/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219)#1,(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72190.500
Maximum likelihood: -68565.63215427783
Running H1
Starting lnL=-70981.390
Maximum likelihood: -68565.66925437303
Starting with D=-0.07420019040000625
Rerunning H1 because of negative LR (D=-0.07420019040000625)
Starting lnL=-68565.632
Maximum likelihood: -68565.63215232383
Rerunning H0, trying to reduce LR (D=3.908004146069288e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63214726099
Rerunning H1 because of negative LR (D=-1.0125688277184963e-05)
Starting lnL=-68565.632
Maximum likelihood: -68565.6321438484
Rerunning H0, trying to reduce LR (D=6.8251683842390776e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63214004171
Rerunning H1 because of negative LR (D=-7.6133874244987965e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.6321341867
Rerunning H0, trying to reduce LR (D=1.1710013495758176e-05)
Starting lnL=-68565.632
Maximum likelihood: -68565.63213333137
Rerunning H1 because of negative LR (D=-1.7106649465858936e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63213196778
Rerunning H0, trying to reduce LR (D=2.7271744329482317e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63212769479
Rerunning H1 because of negative LR (D=-8.545990567654371e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63212674085
Rerunning H0, trying to reduce LR (D=1.907872501760721e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63212491143
Rerunning H1 because of negative LR (D=-3.658846253529191e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63212026953
Rerunning H0, trying to reduce LR (D=9.283801773563027e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.6321199397
Rerunning H1 because of negative LR (D=-6.596383173018694e-07)
Starting lnL=-68565.632
Maximum likelihood: -68565.63211900371
Rerunning H0, trying to reduce LR (D=1.8719874788075686e-06)
Starting lnL=-68565.632
Maximum likelihood: -68565.63211888817
Rerunning H1 because of negative LR (D=-2.310844138264656e-07)
Starting lnL=-68565.632
Maximum likelihood: -68565.63211865687
Performed %!s(MISSING) optimization, finishing
Final D=4.626053851097822e-07
lnL0=-68565.632119, lnL1=-68565.632119
Testing branch 88/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960))#1,ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70872.120
Maximum likelihood: -68565.69038576208
Running H1
Starting lnL=-70800.757
Maximum likelihood: -68565.69047762147
Starting with D=-0.00018371877376921475
Rerunning H1 because of negative LR (D=-0.00018371877376921475)
Starting lnL=-68565.690
Maximum likelihood: -68565.69038532398
Final D=8.761999197304249e-07
lnL0=-68565.690386, lnL1=-68565.690385
Testing branch 89/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410)#1,((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71467.501
Maximum likelihood: -68565.69052444224
Running H1
Starting lnL=-73555.623
Maximum likelihood: -68565.69031794567
Starting with D=0.0004129931330680847
Rerunning H0, trying to reduce LR (D=0.0004129931330680847)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031725242
Rerunning H1 because of negative LR (D=-1.3865064829587936e-06)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031708545
Final D=3.339373506605625e-07
lnL0=-68565.690317, lnL1=-68565.690317
Testing branch 90/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)#1),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-70628.616
Maximum likelihood: -68565.69035163031
Running H1
Starting lnL=-71088.851
Maximum likelihood: -68565.69033281461
Starting with D=3.763139829970896e-05
Rerunning H0, trying to reduce LR (D=3.763139829970896e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69032336435
Rerunning H1 because of negative LR (D=-1.890052226372063e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903233347
Final D=5.931360647082329e-08
lnL0=-68565.690323, lnL1=-68565.690323
Testing branch 91/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337)#1,ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153))))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-71150.710
Maximum likelihood: -68565.69031774715
Running H1
Starting lnL=-71841.934
Maximum likelihood: -68565.69032842111
Starting with D=-2.1347921574488282e-05
Rerunning H1 because of negative LR (D=-2.1347921574488282e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.69031754926
Final D=3.9578299038112164e-07
lnL0=-68565.690318, lnL1=-68565.690318
Testing branch 92/92
Foreground branch: (((((((((ENSAPLP00000009322,ENSABRP00000003006),(((ENSGALP00000004679,ENSCJPP00005024982),ENSMGAP00000002269),ENSNMEP00000016237)),((ENSCPGP00000004132,ENSCPUP00000011082),((ENSCCEP00000026451,ENSPMJP00000001717),(ENSJHYP00000019643,ENSTGUP00000005124)))),((((ENSAHAP00000019736,ENSAOWP00000021191),ENSARWP00000007472),ENSDNVP00000024322),ENSNPEP00000015915)),ENSCPRP00005026789),(((ENSGAGP00000009547,ENSCABP00000029668),ENSCPBP00000035789),ENSPSIP00000003357)),(((ENSACAP00000014433,ENSPVIP00000004833),ENSNSUP00000021730),ENSSMRP00000027494)),((((((((((ENSPSMP00000034045,ENSMICP00000040544),ENSPCOP00000029595),ENSOGAP00000009410),((((((ENSTGEP00000034756,ENSPANP00000001821),ENSMMUP00000064799),ENSCSAP00000016059),((ENSRROP00000035905,ENSRBIP00000040039),ENSPTEP00000002192)),(((ENSPTRP00000065159,ENSPPAP00000003310),ENSP00000311135),ENSGGOP00000028358)),(((ENSCCAP00000031203,ENSSBOP00000019923),ENSCJAP00000054970),ENSANAP00000010148))),(((((ENSCLAP00000015045,ENSODEP00000013430),(ENSCPOP00000015539,ENSCAPP00000017364)),((ENSHGLP00000019641,ENSHGLP00100026044),ENSFDAP00000019306)),((ENSSTOP00000028141,ENSUPAP00010007531),ENSMMMP00000028004)),((ENSCCNP00000030929,ENSDORP00000012189),(((((((((ENSMSIP00000006814,ENSMUSP00000131734),MGP_SPRETEiJ_P0073662),MGP_CAROLIEiJ_P0070955),MGP_PahariEiJ_P0059160),ENSRNOP00000038631),ENSMUGP00000023219),(((((ENSCGRP00001013429,ENSCGRP00015027881),ENSCGRP00000016117),ENSMAUP00000002071),ENSMOCP00000003943),ENSPEMP00000001958)),ENSNGAP00000012664),ENSJJAP00000020671)))),((ENSECAP00000005751,ENSPVAP00000008182),(((((((ENSBTAP00000027206,ENSBIXP00000032910),ENSBIXP00005012921),ENSBMUP00000024247),ENSBBBP00000011829),ENSCHIP00000020552),ENSSSCP00000070027),((((ENSUAMP00000004660,ENSAMEP00000016410),((ENSCAFP00020015672,ENSCAFP00000010337),ENSVVUP00000035960)),ENSNVIP00000028219),(ENSFCAP00000043121,ENSPPRP00000011153)#1)))),ENSLAFP00000003483),ENSDNOP00000002659),ENSPCIP00000025499),ENSOANP00000002114)),ENSXETP00000030036,ENSLACP00000014293);
Running H0
Starting lnL=-72750.895
Maximum likelihood: -68565.69031412022
Running H1
Starting lnL=-71667.107
Maximum likelihood: -68565.6903327776
Starting with D=-3.73147486243397e-05
Rerunning H1 because of negative LR (D=-3.73147486243397e-05)
Starting lnL=-68565.690
Maximum likelihood: -68565.6903141197
Final D=1.0477378964424133e-09
lnL0=-68565.690314, lnL1=-68565.690314
Running time: 14h34m33.531970273s