jModeltest 2.1.

5 -------------------------------

(c) 2011-onwards D. Darriba, G.L. Taboada, R. Doallo and D. Posada,

(1) Department of Biochemistry, Genetics and Immunology

University of Vigo, 36310 Vigo, Spain.

(2) Department of Electronics and Systems

University of A Coruna, 15071 A Coruna, Spain.

e-mail: ddarriba@udc.es, dposada@uvigo.es

--------------------------------------------------------------------------------

Tue Aug 29 13:48:47 COT 2017

Windows 10 10.0, arch: amd64, bits: 64, numcores: 4

jModelTest 2.1.5

Copyright (C) 2011 D. Darriba, G.L. Taboada, R. Doallo and D. Posada

This program comes with ABSOLUTELY NO WARRANTY

This is free software, and you are welcome to redistribute it under certain conditions

Notice: This program may contain errors. Please inspect results carefully.

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Citation: Darriba D, Taboada GL, Doallo R and Posada D. 2012.

"jModelTest 2: more models, new heuristics and parallel computing".

Nature Methods 9(8), 772.

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Reading data file "primate-mtDNA.nex"... OK.

number of sequences: 12

number of sites: 898

---------------------------------------------------------------

* *

* COMPUTATION OF LIKELIHOOD SCORES WITH PHYML *

* *

---------------------------------------------------------------

::Settings::

Phyml version = 3.0

Phyml binary = PhyML_3.0_win32.exe

Phyml path = C:\Users\estudiantes\Downloads\jmodeltest-2.1.5\exe\phyml\

Candidate models = 88

number of substitution schemes = 11

including models with equal/unequal base frequencies (+F)

including models with/without a proportion of invariable sites (+I)

including models with/without rate variation among sites (+G) (nCat = 4)

Optimized free parameters (K) = substitution parameters + 21 branch lengths + topology

Base tree for likelihood calculations = ML tree

Tree topology search operation = NNI

::Progress::

Model Exec. Time Total Time -lnL

-------------------------------------------------------------------------

F81+I+G 00h:00:10:04 00h:00:10:05 6103.9550

HKY+I+G 00h:00:18:04 00h:00:18:04 5711.9390

TPM1uf+I+G 00h:00:21:07 00h:00:21:07 5711.8131

TrN+I+G 00h:00:27:07 00h:00:27:07 5710.5516

TPM2uf+I+G 00h:00:20:07 00h:00:31:02 5710.0931

TPM3uf+I+G 00h:00:21:04 00h:00:39:09 5711.6973

TIM1+I+G 00h:00:26:05 00h:00:48:02 5710.4362

TIM2+I+G 00h:00:21:08 00h:00:49:05 5709.4032

TIM3+I+G 00h:00:23:07 00h:00:55:00 5710.4093

JC+I+G 00h:00:08:08 00h:00:58:03 6269.1483

TVM+I+G 00h:00:23:00 00h:01:02:08 5709.6328

K80+I+G 00h:00:08:05 00h:01:03:04 5950.5760

TPM2+I+G 00h:00:07:08 00h:01:11:02 5875.0360

TrNef+I+G 00h:00:13:09 00h:01:12:02 5898.8328

GTR+I+G 00h:00:27:04 00h:01:15:06 5708.9231

TPM1+I+G 00h:00:13:01 00h:01:15:09 5941.7822

TPM3+I+G 00h:00:13:00 00h:01:24:02 5946.9553

TIM2ef+I+G 00h:00:12:01 00h:01:27:07 5826.8315

TIM1ef+I+G 00h:00:16:01 00h:01:28:03 5889.4633

TIM3ef+I+G 00h:00:12:07 00h:01:28:06 5894.8548

F81+G 00h:00:04:09 00h:01:33:03 6106.1849

TVMef+I+G 00h:00:09:00 00h:01:33:03 5869.3310

HKY+G 00h:00:07:01 00h:01:35:07 5711.9390

TrN+G 00h:00:07:00 00h:01:40:02 5710.5515

TPM1uf+G 00h:00:07:04 00h:01:40:06 5711.8129

SYM+I+G 00h:00:13:03 00h:01:41:00 5820.7526

TPM2uf+G 00h:00:07:04 00h:01:43:00 5710.0931

TPM3uf+G 00h:00:07:05 00h:01:47:07 5711.6972

TIM2+G 00h:00:08:00 00h:01:49:00 5709.4030

TIM1+G 00h:00:08:05 00h:01:49:01 5710.4363

TIM3+G 00h:00:08:05 00h:01:51:05 5710.2579

JC+G 00h:00:03:09 00h:01:53:00 6272.4691

TVM+G 00h:00:08:00 00h:01:55:07 5709.6330

K80+G 00h:00:04:09 00h:01:56:04 5950.8734

TrNef+G 00h:00:05:03 00h:01:58:03 5899.5606

GTR+G 00h:00:11:03 00h:02:00:03 5708.9232

TPM1+G 00h:00:05:00 00h:02:00:07 5942.5809

TPM2+G 00h:00:04:04 00h:02:00:08 5875.4980

TPM3+G 00h:00:05:00 00h:02:03:03 5947.4060

TIM1ef+G 00h:00:05:01 00h:02:05:04 5890.5866

TIM2ef+G 00h:00:04:09 00h:02:05:06 5827.7101

TIM3ef+G 00h:00:05:03 00h:02:06:01 5895.5795

F81+I 00h:00:01:06 00h:02:07:02 6117.4363

TVMef+G 00h:00:04:07 00h:02:08:00 5870.0774

HKY+I 00h:00:02:00 00h:02:08:01 5768.0041

TrN+I 00h:00:02:02 00h:02:09:03 5766.1021

TPM1uf+I 00h:00:02:00 00h:02:10:00 5765.2881

TPM2uf+I 00h:00:02:01 00h:02:10:02 5761.4637

SYM+G 00h:00:05:06 00h:02:11:00 5821.7573

TPM3uf+I 00h:00:02:00 00h:02:11:04 5764.8303

TIM1+I 00h:00:02:03 00h:02:12:04 5763.3193

TIM2+I 00h:00:02:04 00h:02:12:06 5760.8117

TIM3+I 00h:00:02:03 00h:02:13:04 5762.6853

TVM+I 00h:00:02:02 00h:02:13:06 5757.9741

JC+I 00h:00:01:05 00h:02:14:01 6277.7809

K80+I 00h:00:01:07 00h:02:15:01 5974.9052

TrNef+I 00h:00:01:07 00h:02:15:03 5928.0549

GTR+I 00h:00:03:02 00h:02:15:06 5757.2159

TPM1+I 00h:00:01:07 00h:02:15:08 5963.0445

TPM2+I 00h:00:01:07 00h:02:16:08 5900.5165

TPM3+I 00h:00:01:07 00h:02:17:00 5969.5992

TIM1ef+I 00h:00:01:08 00h:02:17:04 5916.3530

TIM2ef+I 00h:00:01:08 00h:02:17:06 5851.7159

TIM3ef+I 00h:00:01:07 00h:02:18:04 5923.0656

TVMef+I 00h:00:01:08 00h:02:18:09 5892.6085

SYM+I 00h:00:01:08 00h:02:19:01 5844.3147

F81 00h:00:01:07 00h:02:19:03 6284.9956

HKY 00h:00:01:08 00h:02:20:03 5981.7202

TrN 00h:00:01:06 00h:02:20:05 5978.8549

TPM1uf 00h:00:01:06 00h:02:20:08 5973.2392

TPM2uf 00h:00:01:06 00h:02:20:09 5953.3750

TPM3uf 00h:00:01:07 00h:02:21:09 5967.2949

TIM1 00h:00:01:06 00h:02:22:01 5970.4894

TIM2 00h:00:01:07 00h:02:22:04 5948.7051

TIM3 00h:00:01:07 00h:02:22:06 5964.6750

TVM 00h:00:01:08 00h:02:23:07 5938.5617

JC 00h:00:01:04 00h:02:23:08 6424.2025

GTR 00h:00:02:00 00h:02:24:01 5934.1469

K80 00h:00:01:08 00h:02:24:04 6142.4291

TrNef 00h:00:01:05 00h:02:25:02 6086.2180

TPM1 00h:00:01:05 00h:02:25:03 6132.1443

TPM2 00h:00:01:06 00h:02:25:06 6058.5032

TPM3 00h:00:01:05 00h:02:25:08 6130.1778

TIM1ef 00h:00:01:05 00h:02:26:08 6075.9424

TIM2ef 00h:00:01:06 00h:02:27:00 6003.1493

TIM3ef 00h:00:01:05 00h:02:27:01 6073.4350

TVMef 00h:00:01:06 00h:02:27:05 6045.3644

SYM 00h:00:01:06 00h:02:28:04 5989.3816

::Results::
Model = JC

partition = 000000

-lnL = 6424.2024

K = 22

Model = JC+I

partition = 000000

-lnL = 6277.7809

K = 23

p-inv = 0.3570

Model = JC+G

partition = 000000

-lnL = 6272.4691

K = 23

gamma shape = 0.7460

Model = JC+I+G

partition = 000000

-lnL = 6269.1483

K = 24

p-inv = 0.2730

gamma shape = 2.5210

Model = F81

partition = 000000

-lnL = 6284.9956

K = 25
freqA = 0.2684

freqC = 0.3038

freqG = 0.1125

freqT = 0.3153

Model = F81+I

partition = 000000

-lnL = 6117.4363

K = 26

freqA = 0.2678

freqC = 0.3205

freqG = 0.1057

freqT = 0.3060

p-inv = 0.3660

Model = F81+G

partition = 000000

-lnL = 6106.1849

K = 26

freqA = 0.2617

freqC = 0.3299

freqG = 0.1045

freqT = 0.3040

gamma shape = 0.6560

Model = F81+I+G

partition = 000000

-lnL = 6103.9550

K = 27
freqA = 0.2629

freqC = 0.3281

freqG = 0.1045

freqT = 0.3044

p-inv = 0.2610

gamma shape = 1.8250

Model = K80

partition = 010010

-lnL = 6142.4291

K = 23

kappa = 4.5721 (ti/tv = 2.2861)

Model = K80+I

partition = 010010

-lnL = 5974.9052

K = 24

kappa = 5.2363 (ti/tv = 2.6182)

p-inv = 0.3680

Model = K80+G

partition = 010010

-lnL = 5950.8734

K = 24

kappa = 6.1846 (ti/tv = 3.0923)

gamma shape = 0.5610

Model = K80+I+G

partition = 010010
-lnL = 5950.5760

K = 25

kappa = 6.1191 (ti/tv = 3.0596)

p-inv = 0.1500

gamma shape = 0.8620

Model = HKY

partition = 010010

-lnL = 5981.7202

K = 26

freqA = 0.3139

freqC = 0.2926

freqG = 0.1040

freqT = 0.2895

kappa = 4.9867 (ti/tv = 2.4056)

Model = HKY+I

partition = 010010

-lnL = 5768.0041

K = 27

freqA = 0.3504

freqC = 0.3076

freqG = 0.0901

freqT = 0.2519

kappa = 6.9917 (ti/tv = 3.0938)

p-inv = 0.3690

Model = HKY+G

partition = 010010
-lnL = 5711.9390

K = 27

freqA = 0.3637

freqC = 0.3199

freqG = 0.0815

freqT = 0.2349

kappa = 12.7212 (ti/tv = 5.3969)

gamma shape = 0.3630

Model = HKY+I+G

partition = 010010

-lnL = 5711.9390

K = 28

freqA = 0.3637

freqC = 0.3199

freqG = 0.0815

freqT = 0.2349

kappa = 12.7350 (ti/tv = 5.4031)

p-inv = 0.0000

gamma shape = 0.3630

Model = TrNef

partition = 010020

-lnL = 6086.2180

K = 24

R(a) [AC] = 1.0000

R(b) [AG] = 2.6202

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 6.2392

R(f) [GT] = 1.0000

Model = TrNef+I

partition = 010020

-lnL = 5928.0549

K = 25

R(a) [AC] = 1.0000

R(b) [AG] = 2.8434

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 7.4096

R(f) [GT] = 1.0000

p-inv = 0.3480

Model = TrNef+G

partition = 010020

-lnL = 5899.5606

K = 25

R(a) [AC] = 1.0000

R(b) [AG] = 2.8871

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 9.8354

R(f) [GT] = 1.0000

gamma shape = 0.5720

Model = TrNef+I+G

partition = 010020
-lnL = 5898.8328

K = 26

R(a) [AC] = 1.0000

R(b) [AG] = 2.8666

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 9.6766

R(f) [GT] = 1.0000

p-inv = 0.1660

gamma shape = 0.9520

Model = TrN

partition = 010020

-lnL = 5978.8549

K = 27

freqA = 0.3243

freqC = 0.2838

freqG = 0.1120

freqT = 0.2799

R(a) [AC] = 1.0000

R(b) [AG] = 4.2130

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 5.4329

R(f) [GT] = 1.0000

Model = TrN+I

partition = 010020

-lnL = 5766.1021
K = 28

freqA = 0.3441

freqC = 0.3134

freqG = 0.0837

freqT = 0.2588

R(a) [AC] = 1.0000

R(b) [AG] = 8.4082

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 6.4457

R(f) [GT] = 1.0000

p-inv = 0.3710

Model = TrN+G

partition = 010020

-lnL = 5710.5514

K = 28

freqA = 0.3581

freqC = 0.3252

freqG = 0.0765

freqT = 0.2402

R(a) [AC] = 1.0000

R(b) [AG] = 15.9685

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 11.6720

R(f) [GT] = 1.0000

gamma shape = 0.3570

Model = TrN+I+G

partition = 010020

-lnL = 5710.5516

K = 29

freqA = 0.3581

freqC = 0.3253

freqG = 0.0765

freqT = 0.2402

R(a) [AC] = 1.0000

R(b) [AG] = 16.0167

R(c) [AT] = 1.0000

R(d) [CG] = 1.0000

R(e) [CT] = 11.6748

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3570

Model = TPM1

partition = 012210

-lnL = 6132.1443

K = 24

R(a) [AC] = 1.0000

R(b) [AG] = 3.4735

R(c) [AT] = 0.5153

R(d) [CG] = 0.5153

R(e) [CT] = 3.4735

R(f) [GT] = 1.0000

Model = TPM1+I
partition = 012210

-lnL = 5963.0445

K = 25

R(a) [AC] = 1.0000

R(b) [AG] = 3.6406

R(c) [AT] = 0.3857

R(d) [CG] = 0.3857

R(e) [CT] = 3.6406

R(f) [GT] = 1.0000

p-inv = 0.3690

Model = TPM1+G

partition = 012210

-lnL = 5942.5809

K = 25

R(a) [AC] = 1.0000

R(b) [AG] = 4.2350

R(c) [AT] = 0.4032

R(d) [CG] = 0.4032

R(e) [CT] = 4.2350

R(f) [GT] = 1.0000

gamma shape = 0.5790

Model = TPM1+I+G

partition = 012210

-lnL = 5941.7822

K = 26

R(a) [AC] = 1.0000

R(b) [AG] = 4.1380

R(c) [AT] = 0.3918

R(d) [CG] = 0.3918

R(e) [CT] = 4.1380

R(f) [GT] = 1.0000

p-inv = 0.2000

gamma shape = 1.0920

Model = TPM1uf

partition = 012210

-lnL = 5973.2392

K = 27

freqA = 0.3128

freqC = 0.2870

freqG = 0.1045

freqT = 0.2957

R(a) [AC] = 1.0000

R(b) [AG] = 3.8629

R(c) [AT] = 0.5436

R(d) [CG] = 0.5436

R(e) [CT] = 3.8629

R(f) [GT] = 1.0000

Model = TPM1uf+I

partition = 012210

-lnL = 5765.2881

K = 28

freqA = 0.3486

freqC = 0.3049

freqG = 0.0910
freqT = 0.2555

R(a) [AC] = 1.0000

R(b) [AG] = 5.7106

R(c) [AT] = 0.6120

R(d) [CG] = 0.6120

R(e) [CT] = 5.7106

R(f) [GT] = 1.0000

p-inv = 0.3690

Model = TPM1uf+G

partition = 012210

-lnL = 5711.8129

K = 28

freqA = 0.3633

freqC = 0.3190

freqG = 0.0817

freqT = 0.2359

R(a) [AC] = 1.0000

R(b) [AG] = 11.7940

R(c) [AT] = 0.8518

R(d) [CG] = 0.8518

R(e) [CT] = 11.7940

R(f) [GT] = 1.0000

gamma shape = 0.3650

Model = TPM1uf+I+G

partition = 012210

-lnL = 5711.8131

K = 29
freqA = 0.3633

freqC = 0.3190

freqG = 0.0817

freqT = 0.2359

R(a) [AC] = 1.0000

R(b) [AG] = 11.7966

R(c) [AT] = 0.8515

R(d) [CG] = 0.8515

R(e) [CT] = 11.7966

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3650

Model = TPM2

partition = 010212

-lnL = 6058.5032

K = 24

R(a) [AC] = 14.0258

R(b) [AG] = 40.7837

R(c) [AT] = 14.0258

R(d) [CG] = 1.0000

R(e) [CT] = 40.7837

R(f) [GT] = 1.0000

Model = TPM2+I

partition = 010212

-lnL = 5900.5165

K = 25

R(a) [AC] = 29.6121

R(b) [AG] = 93.1600

R(c) [AT] = 29.6121

R(d) [CG] = 1.0000

R(e) [CT] = 93.1600

R(f) [GT] = 1.0000

p-inv = 0.3580

Model = TPM2+G

partition = 010212

-lnL = 5875.4980

K = 25

R(a) [AC] = 93.0390

R(b) [AG] = 308.1144

R(c) [AT] = 93.0390

R(d) [CG] = 1.0000

R(e) [CT] = 308.1144

R(f) [GT] = 1.0000

gamma shape = 0.6180

Model = TPM2+I+G

partition = 010212

-lnL = 5875.0360

K = 26

R(a) [AC] = 110.3883

R(b) [AG] = 363.7570

R(c) [AT] = 110.3883

R(d) [CG] = 1.0000

R(e) [CT] = 363.7570

R(f) [GT] = 1.0000

p-inv = 0.1620

gamma shape = 1.0090

Model = TPM2uf

partition = 010212

-lnL = 5953.3750

K = 27

freqA = 0.2971

freqC = 0.2939

freqG = 0.1184

freqT = 0.2905

R(a) [AC] = 4.8622

R(b) [AG] = 18.8807

R(c) [AT] = 4.8622

R(d) [CG] = 1.0000

R(e) [CT] = 18.8807

R(f) [GT] = 1.0000

Model = TPM2uf+I

partition = 010212

-lnL = 5761.4637

K = 28

freqA = 0.3399

freqC = 0.3086

freqG = 0.0979

freqT = 0.2536

R(a) [AC] = 2.7437

R(b) [AG] = 16.1770

R(c) [AT] = 2.7437

R(d) [CG] = 1.0000

R(e) [CT] = 16.1770

R(f) [GT] = 1.0000

p-inv = 0.3720

Model = TPM2uf+G

partition = 010212

-lnL = 5710.0931

K = 28

freqA = 0.3585

freqC = 0.3207

freqG = 0.0844

freqT = 0.2365

R(a) [AC] = 2.0800

R(b) [AG] = 22.7759

R(c) [AT] = 2.0800

R(d) [CG] = 1.0000

R(e) [CT] = 22.7759

R(f) [GT] = 1.0000

gamma shape = 0.3720

Model = TPM2uf+I+G

partition = 010212

-lnL = 5710.0931

K = 29

freqA = 0.3584

freqC = 0.3207

freqG = 0.0844

freqT = 0.2365
R(a) [AC] = 2.0806

R(b) [AG] = 22.8019

R(c) [AT] = 2.0806

R(d) [CG] = 1.0000

R(e) [CT] = 22.8019

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3710

Model = TPM3

partition = 012012

-lnL = 6130.1778

K = 24

R(a) [AC] = 1.8982

R(b) [AG] = 6.7257

R(c) [AT] = 1.0000

R(d) [CG] = 1.8982

R(e) [CT] = 6.7257

R(f) [GT] = 1.0000

Model = TPM3+I

partition = 012012

-lnL = 5969.5992

K = 25

R(a) [AC] = 1.6418

R(b) [AG] = 7.0730

R(c) [AT] = 1.0000

R(d) [CG] = 1.6418

R(e) [CT] = 7.0730

R(f) [GT] = 1.0000

p-inv = 0.3650

Model = TPM3+G

partition = 012012

-lnL = 5947.4060

K = 25

R(a) [AC] = 1.6041

R(b) [AG] = 8.1360

R(c) [AT] = 1.0000

R(d) [CG] = 1.6041

R(e) [CT] = 8.1360

R(f) [GT] = 1.0000

gamma shape = 0.5760

Model = TPM3+I+G

partition = 012012

-lnL = 5946.9553

K = 26

R(a) [AC] = 1.6138

R(b) [AG] = 8.0761

R(c) [AT] = 1.0000

R(d) [CG] = 1.6138

R(e) [CT] = 8.0761

R(f) [GT] = 1.0000

p-inv = 0.1580

gamma shape = 0.9170

Model = TPM3uf
partition = 012012

-lnL = 5967.2949

K = 27

freqA = 0.3125

freqC = 0.2788

freqG = 0.1037

freqT = 0.3050

R(a) [AC] = 2.1583

R(b) [AG] = 7.8752

R(c) [AT] = 1.0000

R(d) [CG] = 2.1583

R(e) [CT] = 7.8752

R(f) [GT] = 1.0000

Model = TPM3uf+I

partition = 012012

-lnL = 5764.8303

K = 28

freqA = 0.3495

freqC = 0.3035

freqG = 0.0901

freqT = 0.2569

R(a) [AC] = 1.5872

R(b) [AG] = 9.2413

R(c) [AT] = 1.0000

R(d) [CG] = 1.5872

R(e) [CT] = 9.2413

R(f) [GT] = 1.0000

p-inv = 0.3680
Model = TPM3uf+G

partition = 012012

-lnL = 5711.6972

K = 28

freqA = 0.3635

freqC = 0.3180

freqG = 0.0817

freqT = 0.2368

R(a) [AC] = 1.2268

R(b) [AG] = 14.2408

R(c) [AT] = 1.0000

R(d) [CG] = 1.2268

R(e) [CT] = 14.2408

R(f) [GT] = 1.0000

gamma shape = 0.3660

Model = TPM3uf+I+G

partition = 012012

-lnL = 5711.6973

K = 29

freqA = 0.3635

freqC = 0.3181

freqG = 0.0817

freqT = 0.2368

R(a) [AC] = 1.2276

R(b) [AG] = 14.2676

R(c) [AT] = 1.0000

R(d) [CG] = 1.2276

R(e) [CT] = 14.2676

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3660

Model = TIM1ef

partition = 012230

-lnL = 6075.9424

K = 25

R(a) [AC] = 1.0000

R(b) [AG] = 1.9924

R(c) [AT] = 0.5154

R(d) [CG] = 0.5154

R(e) [CT] = 4.7382

R(f) [GT] = 1.0000

Model = TIM1ef+I

partition = 012230

-lnL = 5916.3530

K = 26

R(a) [AC] = 1.0000

R(b) [AG] = 1.9931

R(c) [AT] = 0.3945

R(d) [CG] = 0.3945

R(e) [CT] = 5.1790

R(f) [GT] = 1.0000

p-inv = 0.3490

Model = TIM1ef+G
partition = 012230

-lnL = 5890.5866

K = 26

R(a) [AC] = 1.0000

R(b) [AG] = 1.9663

R(c) [AT] = 0.3766

R(d) [CG] = 0.3766

R(e) [CT] = 6.6156

R(f) [GT] = 1.0000

gamma shape = 0.5850

Model = TIM1ef+I+G

partition = 012230

-lnL = 5889.4633

K = 27

R(a) [AC] = 1.0000

R(b) [AG] = 1.9406

R(c) [AT] = 0.3690

R(d) [CG] = 0.3690

R(e) [CT] = 6.4525

R(f) [GT] = 1.0000

p-inv = 0.1900

gamma shape = 1.0830

Model = TIM1

partition = 012230

-lnL = 5970.4894

K = 28

freqA = 0.3230
freqC = 0.2789

freqG = 0.1126

freqT = 0.2856

R(a) [AC] = 1.0000

R(b) [AG] = 3.2806

R(c) [AT] = 0.5461

R(d) [CG] = 0.5461

R(e) [CT] = 4.2101

R(f) [GT] = 1.0000

Model = TIM1+I

partition = 012230

-lnL = 5763.3193

K = 29

freqA = 0.3424

freqC = 0.3103

freqG = 0.0843

freqT = 0.2630

R(a) [AC] = 1.0000

R(b) [AG] = 6.8885

R(c) [AT] = 0.6077

R(d) [CG] = 0.6077

R(e) [CT] = 5.2393

R(f) [GT] = 1.0000

p-inv = 0.3710

Model = TIM1+G

partition = 012230

-lnL = 5710.4362
K = 29

freqA = 0.3578

freqC = 0.3243

freqG = 0.0767

freqT = 0.2412

R(a) [AC] = 1.0000

R(b) [AG] = 14.8203

R(c) [AT] = 0.8592

R(d) [CG] = 0.8592

R(e) [CT] = 10.8556

R(f) [GT] = 1.0000

gamma shape = 0.3590

Model = TIM1+I+G

partition = 012230

-lnL = 5710.4362

K = 30

freqA = 0.3578

freqC = 0.3243

freqG = 0.0766

freqT = 0.2413

R(a) [AC] = 1.0000

R(b) [AG] = 14.8854

R(c) [AT] = 0.8602

R(d) [CG] = 0.8602

R(e) [CT] = 10.8619

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3590

Model = TIM2ef

partition = 010232

-lnL = 6003.1493

K = 25

R(a) [AC] = 9.9294

R(b) [AG] = 17.2577

R(c) [AT] = 9.9294

R(d) [CG] = 1.0000

R(e) [CT] = 40.4329

R(f) [GT] = 1.0000

Model = TIM2ef+I

partition = 010232

-lnL = 5851.7158

K = 26

R(a) [AC] = 12.9303

R(b) [AG] = 23.6190

R(c) [AT] = 12.9303

R(d) [CG] = 1.0000

R(e) [CT] = 60.9573

R(f) [GT] = 1.0000

p-inv = 0.3450

Model = TIM2ef+G

partition = 010232

-lnL = 5827.7101

K = 26

R(a) [AC] = 15.3540

R(b) [AG] = 28.2994

R(c) [AT] = 15.3540

R(d) [CG] = 1.0000

R(e) [CT] = 87.4862

R(f) [GT] = 1.0000

gamma shape = 0.6140

Model = TIM2ef+I+G

partition = 010232

-lnL = 5826.8315

K = 27

R(a) [AC] = 15.3180

R(b) [AG] = 28.0989

R(c) [AT] = 15.3180

R(d) [CG] = 1.0000

R(e) [CT] = 86.3955

R(f) [GT] = 1.0000

p-inv = 0.1700

gamma shape = 1.0510

Model = TIM2

partition = 010232

-lnL = 5948.7051

K = 28

freqA = 0.3073

freqC = 0.2821

freqG = 0.1328

freqT = 0.2778

R(a) [AC] = 4.9004

R(b) [AG] = 15.1371

R(c) [AT] = 4.9004

R(d) [CG] = 1.0000

R(e) [CT] = 21.0670

R(f) [GT] = 1.0000

Model = TIM2+I

partition = 010232

-lnL = 5760.8117

K = 29

freqA = 0.3382

freqC = 0.3121

freqG = 0.0922

freqT = 0.2576

R(a) [AC] = 2.5880

R(b) [AG] = 17.4329

R(c) [AT] = 2.5880

R(d) [CG] = 1.0000

R(e) [CT] = 14.7120

R(f) [GT] = 1.0000

p-inv = 0.3740

Model = TIM2+G

partition = 010232

-lnL = 5709.4030

K = 29

freqA = 0.3555

freqC = 0.3245

freqG = 0.0799
freqT = 0.2401

R(a) [AC] = 1.8762

R(b) [AG] = 24.8154

R(c) [AT] = 1.8762

R(d) [CG] = 1.0000

R(e) [CT] = 19.7516

R(f) [GT] = 1.0000

gamma shape = 0.3650

Model = TIM2+I+G

partition = 010232

-lnL = 5709.4032

K = 30

freqA = 0.3554

freqC = 0.3245

freqG = 0.0799

freqT = 0.2401

R(a) [AC] = 1.8782

R(b) [AG] = 24.8337

R(c) [AT] = 1.8782

R(d) [CG] = 1.0000

R(e) [CT] = 19.7688

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3650

Model = TIM3ef

partition = 012032

-lnL = 6073.4350
K = 25

R(a) [AC] = 2.0066

R(b) [AG] = 3.9819

R(c) [AT] = 1.0000

R(d) [CG] = 2.0066

R(e) [CT] = 9.5250

R(f) [GT] = 1.0000

Model = TIM3ef+I

partition = 012032

-lnL = 5923.0656

K = 26

R(a) [AC] = 1.7008

R(b) [AG] = 3.9259

R(c) [AT] = 1.0000

R(d) [CG] = 1.7008

R(e) [CT] = 10.1994

R(f) [GT] = 1.0000

p-inv = 0.3450

Model = TIM3ef+G

partition = 012032

-lnL = 5895.5795

K = 26

R(a) [AC] = 1.8320

R(b) [AG] = 4.1382

R(c) [AT] = 1.0000

R(d) [CG] = 1.8320

R(e) [CT] = 14.0589

R(f) [GT] = 1.0000

gamma shape = 0.5860

Model = TIM3ef+I+G

partition = 012032

-lnL = 5894.8548

K = 27

R(a) [AC] = 1.8197

R(b) [AG] = 4.0944

R(c) [AT] = 1.0000

R(d) [CG] = 1.8197

R(e) [CT] = 13.7501

R(f) [GT] = 1.0000

p-inv = 0.1670

gamma shape = 0.9830

Model = TIM3

partition = 012032

-lnL = 5964.6750

K = 28

freqA = 0.3225

freqC = 0.2718

freqG = 0.1114

freqT = 0.2943

R(a) [AC] = 2.1585

R(b) [AG] = 6.7069

R(c) [AT] = 1.0000

R(d) [CG] = 2.1585

R(e) [CT] = 8.5608

R(f) [GT] = 1.0000

Model = TIM3+I

partition = 012032

-lnL = 5762.6853

K = 29

freqA = 0.3427

freqC = 0.3090

freqG = 0.0834

freqT = 0.2650

R(a) [AC] = 1.6011

R(b) [AG] = 11.2986

R(c) [AT] = 1.0000

R(d) [CG] = 1.6011

R(e) [CT] = 8.5039

R(f) [GT] = 1.0000

p-inv = 0.3710

Model = TIM3+G

partition = 012032

-lnL = 5710.2579

K = 29

freqA = 0.3577

freqC = 0.3232

freqG = 0.0765

freqT = 0.2425

R(a) [AC] = 1.2435

R(b) [AG] = 18.0423

R(c) [AT] = 1.0000

R(d) [CG] = 1.2435

R(e) [CT] = 13.1273

R(f) [GT] = 1.0000

gamma shape = 0.3600

Model = TIM3+I+G

partition = 012032

-lnL = 5710.4093

K = 30

freqA = 0.3578

freqC = 0.3229

freqG = 0.0758

freqT = 0.2435

R(a) [AC] = 1.2547

R(b) [AG] = 18.4046

R(c) [AT] = 1.0000

R(d) [CG] = 1.2547

R(e) [CT] = 12.8444

R(f) [GT] = 1.0000

p-inv = 0.0960

gamma shape = 0.4530

Model = TVMef

partition = 012314

-lnL = 6045.3644

K = 26

R(a) [AC] = 33.6323

R(b) [AG] = 75.4599

R(c) [AT] = 17.5827

R(d) [CG] = 2.6416

R(e) [CT] = 75.4599

R(f) [GT] = 1.0000

Model = TVMef+I

partition = 012314

-lnL = 5892.6085

K = 27

R(a) [AC] = 39.1272

R(b) [AG] = 96.8918

R(c) [AT] = 21.2007

R(d) [CG] = 0.8747

R(e) [CT] = 96.8918

R(f) [GT] = 1.0000

p-inv = 0.3560

Model = TVMef+G

partition = 012314

-lnL = 5870.0774

K = 27

R(a) [AC] = 300.6068

R(b) [AG] = 796.1793

R(c) [AT] = 173.3351

R(d) [CG] = 4.1276

R(e) [CT] = 796.1793

R(f) [GT] = 1.0000

gamma shape = 0.6370

Model = TVMef+I+G
partition = 012314

-lnL = 5869.3309

K = 28

R(a) [AC] = 311.2112

R(b) [AG] = 814.9956

R(c) [AT] = 176.8926

R(d) [CG] = 3.1785

R(e) [CT] = 814.9956

R(f) [GT] = 1.0000

p-inv = 0.1850

gamma shape = 1.1510

Model = TVM

partition = 012314

-lnL = 5938.5617

K = 29

freqA = 0.2954

freqC = 0.2793

freqG = 0.1185

freqT = 0.3069

R(a) [AC] = 14.9113

R(b) [AG] = 42.6773

R(c) [AT] = 7.0967

R(d) [CG] = 3.5569

R(e) [CT] = 42.6773

R(f) [GT] = 1.0000

Model = TVM+I

partition = 012314
-lnL = 5757.9741

K = 30

freqA = 0.3385

freqC = 0.3040

freqG = 0.0983

freqT = 0.2592

R(a) [AC] = 5.7788

R(b) [AG] = 28.3784

R(c) [AT] = 3.6953

R(d) [CG] = 2.3263

R(e) [CT] = 28.3784

R(f) [GT] = 1.0000

p-inv = 0.3710

Model = TVM+G

partition = 012314

-lnL = 5709.6330

K = 30

freqA = 0.3580

freqC = 0.3186

freqG = 0.0846

freqT = 0.2388

R(a) [AC] = 4.0286

R(b) [AG] = 40.7430

R(c) [AT] = 3.4376

R(d) [CG] = 2.4119

R(e) [CT] = 40.7430

R(f) [GT] = 1.0000

gamma shape = 0.3760

Model = TVM+I+G

partition = 012314

-lnL = 5709.6328

K = 31

freqA = 0.3580

freqC = 0.3186

freqG = 0.0846

freqT = 0.2388

R(a) [AC] = 4.0664

R(b) [AG] = 41.1577

R(c) [AT] = 3.4651

R(d) [CG] = 2.4341

R(e) [CT] = 41.1577

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3760

Model = SYM

partition = 012345

-lnL = 5989.3816

K = 27

R(a) [AC] = 27.2379

R(b) [AG] = 35.7775

R(c) [AT] = 13.5697

R(d) [CG] = 3.1062

R(e) [CT] = 84.2967

R(f) [GT] = 1.0000

Model = SYM+I

partition = 012345

-lnL = 5844.3147

K = 28

R(a) [AC] = 24.2305

R(b) [AG] = 34.4474

R(c) [AT] = 12.6594

R(d) [CG] = 1.7469

R(e) [CT] = 88.4757

R(f) [GT] = 1.0000

p-inv = 0.3420

Model = SYM+G

partition = 012345

-lnL = 5821.7573

K = 28

R(a) [AC] = 40.5938

R(b) [AG] = 56.9408

R(c) [AT] = 20.4892

R(d) [CG] = 2.8936

R(e) [CT] = 175.6031

R(f) [GT] = 1.0000

gamma shape = 0.6320

Model = SYM+I+G

partition = 012345

-lnL = 5820.7526

K = 29

R(a) [AC] = 38.5841

R(b) [AG] = 53.8405

R(c) [AT] = 19.3845

R(d) [CG] = 2.6890

R(e) [CT] = 164.5331

R(f) [GT] = 1.0000

p-inv = 0.1820

gamma shape = 1.1500

Model = GTR

partition = 012345

-lnL = 5934.1469

K = 30

freqA = 0.3052

freqC = 0.2696

freqG = 0.1324

freqT = 0.2928

R(a) [AC] = 15.0988

R(b) [AG] = 34.6651

R(c) [AT] = 7.1901

R(d) [CG] = 3.5755

R(e) [CT] = 47.7546

R(f) [GT] = 1.0000

Model = GTR+I

partition = 012345

-lnL = 5757.2158

K = 31

freqA = 0.3366

freqC = 0.3074
freqG = 0.0920

freqT = 0.2639

R(a) [AC] = 5.4413

R(b) [AG] = 30.8272

R(c) [AT] = 3.4700

R(d) [CG] = 2.3370

R(e) [CT] = 25.6479

R(f) [GT] = 1.0000

p-inv = 0.3730

Model = GTR+G

partition = 012345

-lnL = 5708.9232

K = 31

freqA = 0.3550

freqC = 0.3223

freqG = 0.0801

freqT = 0.2426

R(a) [AC] = 3.5834

R(b) [AG] = 43.6468

R(c) [AT] = 3.0439

R(d) [CG] = 2.3544

R(e) [CT] = 34.7220

R(f) [GT] = 1.0000

gamma shape = 0.3690

Model = GTR+I+G

partition = 012345

-lnL = 5708.9231
 K = 32

freqA = 0.3549

freqC = 0.3224

freqG = 0.0801

freqT = 0.2427

R(a) [AC] = 3.6085

R(b) [AG] = 44.0442

R(c) [AT] = 3.0606

R(d) [CG] = 2.3782

R(e) [CT] = 34.9616

R(f) [GT] = 1.0000

p-inv = 0.0000

gamma shape = 0.3690

Computation of likelihood scores completed. It took 00h:02:28:05.