-------------------------- jModeltest 2.1.6 v20140903 -------------------------- (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 -------------------------------------------------------------------------------- Wed Sep 17 07:31:18 PDT 2014 Linux 2.6.32-431.20.3.el6.x86_64, arch: amd64, bits: 64, numcores: 16 -------------------------------------------------------------------------------- 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. -------------------------------------------------------------------------------- jModelTest 2.1.6 v20140903 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. Arguments = -tr 8 -d infile.phy -s 11 -f -i -g 4 -t fixed -AIC -AICc -BIC -DT -hLRT -O ftvwxgp -p -a -w Reading data file "infile.phy"... OK. number of sequences: 6 number of sites: 631 --------------------------------------------------------------- * * * COMPUTATION OF LIKELIHOOD SCORES WITH PHYML * * * --------------------------------------------------------------- ::Settings:: Phyml version = 20120412 Phyml binary = phyml Phyml path = /opt/jmodeltest2/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 + 9 branch lengths Base tree for likelihood calculations = fixed BIONJ-JC tree topology Estimating a BIONJ-JC tree ... JC 00h:00:00:00 00h:00:00:01 1115.6846 (1/0) OK JC tree: (((P4:0.00669475,(P6:0.00622996,P1:0.00013634):0.00274602):0.00211842,P5:0.00750652):0.00775404,P3:0.01229404,P2:0.00697065); ::Progress:: Model Exec. Time Total Time -lnL ------------------------------------------------------------------------- F81+I+G 00h:00:00:00 00h:00:00:01 1055.3705 (2/88) TPM3uf+I+G 00h:00:00:00 00h:00:00:01 1054.6733 (3/88) HKY+I+G 00h:00:00:00 00h:00:00:01 1054.8627 (4/88) TPM1uf+I+G 00h:00:00:00 00h:00:00:01 1054.7937 (5/88) TPM2uf+I+G 00h:00:00:00 00h:00:00:01 1054.3109 (6/88) TIM2+I+G 00h:00:00:00 00h:00:00:01 1053.7735 (7/88) TrN+I+G 00h:00:00:00 00h:00:00:01 1054.3085 (8/88) TIM1+I+G 00h:00:00:00 00h:00:00:01 1054.2374 (9/88) JC+I+G 00h:00:00:00 00h:00:00:01 1105.3179 (10/88) K80+I+G 00h:00:00:00 00h:00:00:01 1104.8640 (11/88) TIM3+I+G 00h:00:00:00 00h:00:00:01 1054.1076 (12/88) TrNef+I+G 00h:00:00:00 00h:00:00:01 1104.7832 (13/88) TVM+I+G 00h:00:00:00 00h:00:00:01 1054.1197 (14/88) TPM2+I+G 00h:00:00:00 00h:00:00:01 1104.8147 (15/88) TPM1+I+G 00h:00:00:00 00h:00:00:01 1104.8628 (16/88) GTR+I+G 00h:00:00:00 00h:00:00:01 1053.5709 (17/88) TPM3+I+G 00h:00:00:00 00h:00:00:01 1104.8631 (18/88) TIM1ef+I+G 00h:00:00:00 00h:00:00:02 1104.7820 (19/88) TIM2ef+I+G 00h:00:00:00 00h:00:00:02 1104.7365 (20/88) TIM3ef+I+G 00h:00:00:00 00h:00:00:02 1104.7825 (21/88) TVMef+I+G 00h:00:00:00 00h:00:00:02 1104.8121 (22/88) F81+G 00h:00:00:00 00h:00:00:02 1056.5453 (23/88) SYM+I+G 00h:00:00:00 00h:00:00:02 1104.7340 (24/88) HKY+G 00h:00:00:00 00h:00:00:02 1056.0321 (25/88) TrN+G 00h:00:00:00 00h:00:00:02 1055.4711 (26/88) TPM1uf+G 00h:00:00:00 00h:00:00:02 1055.9633 (27/88) TPM3uf+G 00h:00:00:00 00h:00:00:02 1055.8414 (28/88) TPM2uf+G 00h:00:00:00 00h:00:00:02 1055.4684 (29/88) TIM1+G 00h:00:00:00 00h:00:00:02 1055.4008 (30/88) TIM2+G 00h:00:00:01 00h:00:00:02 1054.9223 (31/88) JC+G 00h:00:00:00 00h:00:00:02 1106.5455 (32/88) TVM+G 00h:00:00:00 00h:00:00:02 1055.2762 (33/88) TIM3+G 00h:00:00:01 00h:00:00:02 1055.2704 (34/88) K80+G 00h:00:00:00 00h:00:00:02 1106.0862 (35/88) TrNef+G 00h:00:00:00 00h:00:00:02 1106.0052 (36/88) GTR+G 00h:00:00:01 00h:00:00:03 1054.7203 (37/88) TPM1+G 00h:00:00:00 00h:00:00:03 1106.0854 (38/88) TPM2+G 00h:00:00:00 00h:00:00:03 1106.0467 (39/88) TPM3+G 00h:00:00:00 00h:00:00:03 1106.0862 (40/88) F81+I 00h:00:00:00 00h:00:00:03 1063.8407 (41/88) TIM1ef+G 00h:00:00:00 00h:00:00:03 1106.0043 (42/88) TrN+I 00h:00:00:00 00h:00:00:03 1062.7841 (43/88) HKY+I 00h:00:00:00 00h:00:00:03 1063.3147 (44/88) TIM2ef+G 00h:00:00:00 00h:00:00:03 1105.9646 (45/88) TPM1uf+I 00h:00:00:00 00h:00:00:03 1063.2547 (46/88) TPM2uf+I 00h:00:00:00 00h:00:00:03 1062.7429 (47/88) TIM3ef+G 00h:00:00:00 00h:00:00:03 1106.0051 (48/88) TPM3uf+I 00h:00:00:00 00h:00:00:03 1063.1429 (49/88) TIM1+I 00h:00:00:00 00h:00:00:03 1062.7237 (50/88) TIM2+I 00h:00:00:00 00h:00:00:03 1062.2186 (51/88) TVMef+G 00h:00:00:00 00h:00:00:03 1106.0465 (52/88) TVM+I 00h:00:00:00 00h:00:00:03 1062.5693 (53/88) TIM3+I 00h:00:00:00 00h:00:00:03 1062.6090 (54/88) JC+I 00h:00:00:00 00h:00:00:03 1113.9543 (55/88) GTR+I 00h:00:00:00 00h:00:00:03 1062.0417 (56/88) SYM+G 00h:00:00:00 00h:00:00:03 1105.9644 (57/88) K80+I 00h:00:00:00 00h:00:00:03 1113.4795 (58/88) TrNef+I 00h:00:00:00 00h:00:00:03 1113.4381 (59/88) TPM1+I 00h:00:00:00 00h:00:00:03 1113.4794 (60/88) TPM3+I 00h:00:00:00 00h:00:00:03 1113.4762 (61/88) TPM2+I 00h:00:00:00 00h:00:00:03 1113.4693 (62/88) TIM1ef+I 00h:00:00:00 00h:00:00:03 1113.4381 (63/88) TIM2ef+I 00h:00:00:00 00h:00:00:03 1113.4278 (64/88) TIM3ef+I 00h:00:00:00 00h:00:00:03 1113.4349 (65/88) TVMef+I 00h:00:00:00 00h:00:00:03 1113.4661 (66/88) F81 00h:00:00:00 00h:00:00:03 1065.5537 (67/88) HKY 00h:00:00:00 00h:00:00:03 1065.0272 (68/88) SYM+I 00h:00:00:00 00h:00:00:03 1113.4246 (69/88) TrN 00h:00:00:00 00h:00:00:03 1064.4997 (70/88) TPM1uf 00h:00:00:00 00h:00:00:03 1064.9670 (71/88) JC 00h:00:00:00 00h:00:00:03 1115.6846 (72/88) TPM3uf 00h:00:00:00 00h:00:00:03 1064.8545 (73/88) TPM2uf 00h:00:00:00 00h:00:00:03 1064.4579 (74/88) TIM1 00h:00:00:00 00h:00:00:03 1064.4392 (75/88) TIM2 00h:00:00:00 00h:00:00:03 1063.9345 (76/88) TIM3 00h:00:00:00 00h:00:00:03 1064.3246 (77/88) K80 00h:00:00:00 00h:00:00:03 1115.2090 (78/88) TVM 00h:00:00:00 00h:00:00:03 1064.2834 (79/88) GTR 00h:00:00:00 00h:00:00:03 1063.7577 (80/88) TPM1 00h:00:00:00 00h:00:00:03 1115.2090 (81/88) TrNef 00h:00:00:00 00h:00:00:03 1115.1348 (82/88) TPM2 00h:00:00:00 00h:00:00:03 1115.1681 (83/88) TPM3 00h:00:00:00 00h:00:00:03 1115.2084 (84/88) TIM1ef 00h:00:00:00 00h:00:00:03 1115.1348 (85/88) TIM2ef 00h:00:00:00 00h:00:00:03 1115.0964 (86/88) TVMef 00h:00:00:00 00h:00:00:03 1115.1675 (87/88) TIM3ef 00h:00:00:00 00h:00:00:03 1115.1341 (88/88) SYM 00h:00:00:00 00h:00:00:03 1115.0957 (89/88) Model = JC partition = 000000 -lnL = 1115.6846 K = 9 Model = JC+I partition = 000000 -lnL = 1113.9543 K = 10 p-inv = 0.3000 Model = JC+G partition = 000000 -lnL = 1106.5455 K = 10 gamma shape = 0.0230 Model = JC+I+G partition = 000000 -lnL = 1105.3179 K = 11 p-inv = 0.2780 gamma shape = 0.0110 Model = F81 partition = 000000 -lnL = 1065.5537 K = 12 freqA = 0.4207 freqC = 0.1546 freqG = 0.2019 freqT = 0.2229 Model = F81+I partition = 000000 -lnL = 1063.8407 K = 13 freqA = 0.4211 freqC = 0.1544 freqG = 0.2017 freqT = 0.2227 p-inv = 0.2980 Model = F81+G partition = 000000 -lnL = 1056.5452 K = 13 freqA = 0.4203 freqC = 0.1547 freqG = 0.2022 freqT = 0.2229 gamma shape = 0.0230 Model = F81+I+G partition = 000000 -lnL = 1055.3705 K = 14 freqA = 0.4206 freqC = 0.1546 freqG = 0.2021 freqT = 0.2228 p-inv = 0.2740 gamma shape = 0.0100 Model = K80 partition = 010010 -lnL = 1115.2090 K = 10 kappa = 0.6914 (ti/tv = 0.3457) Model = K80+I partition = 010010 -lnL = 1113.4795 K = 11 kappa = 0.6913 (ti/tv = 0.3456) p-inv = 0.3000 Model = K80+G partition = 010010 -lnL = 1106.0862 K = 11 kappa = 0.6904 (ti/tv = 0.3452) gamma shape = 0.0230 Model = K80+I+G partition = 010010 -lnL = 1104.8639 K = 12 kappa = 0.6903 (ti/tv = 0.3452) p-inv = 0.2780 gamma shape = 0.0110 Model = HKY partition = 010010 -lnL = 1065.0272 K = 13 freqA = 0.4208 freqC = 0.1543 freqG = 0.2028 freqT = 0.2222 kappa = 0.6779 (ti/tv = 0.3454) Model = HKY+I partition = 010010 -lnL = 1063.3147 K = 14 freqA = 0.4212 freqC = 0.1541 freqG = 0.2027 freqT = 0.2219 kappa = 0.6774 (ti/tv = 0.3453) p-inv = 0.2980 Model = HKY+G partition = 010010 -lnL = 1056.0321 K = 14 freqA = 0.4204 freqC = 0.1544 freqG = 0.2030 freqT = 0.2222 kappa = 0.6738 (ti/tv = 0.3434) gamma shape = 0.0230 Model = HKY+I+G partition = 010010 -lnL = 1054.8627 K = 15 freqA = 0.4207 freqC = 0.1543 freqG = 0.2030 freqT = 0.2220 kappa = 0.6737 (ti/tv = 0.3435) p-inv = 0.2740 gamma shape = 0.0100 Model = TrNef partition = 010020 -lnL = 1115.1348 K = 11 R(a) [AC] = 1.0000 R(b) [AG] = 0.6212 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 0.8054 R(f) [GT] = 1.0000 Model = TrNef+I partition = 010020 -lnL = 1113.4381 K = 12 R(a) [AC] = 1.0000 R(b) [AG] = 0.6367 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 0.7745 R(f) [GT] = 1.0000 p-inv = 0.2950 Model = TrNef+G partition = 010020 -lnL = 1106.0051 K = 12 R(a) [AC] = 1.0000 R(b) [AG] = 0.6139 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 0.8165 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TrNef+I+G partition = 010020 -lnL = 1104.7832 K = 13 R(a) [AC] = 1.0000 R(b) [AG] = 0.6330 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 0.7776 R(f) [GT] = 1.0000 p-inv = 0.2800 gamma shape = 0.0110 Model = TrN partition = 010020 -lnL = 1064.4997 K = 14 freqA = 0.4219 freqC = 0.1531 freqG = 0.2039 freqT = 0.2210 R(a) [AC] = 1.0000 R(b) [AG] = 0.5231 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 1.0700 R(f) [GT] = 1.0000 Model = TrN+I partition = 010020 -lnL = 1062.7841 K = 15 freqA = 0.4226 freqC = 0.1528 freqG = 0.2040 freqT = 0.2206 R(a) [AC] = 1.0000 R(b) [AG] = 0.5213 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 1.0718 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = TrN+G partition = 010020 -lnL = 1055.4711 K = 15 freqA = 0.4216 freqC = 0.1532 freqG = 0.2042 freqT = 0.2210 R(a) [AC] = 1.0000 R(b) [AG] = 0.5081 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 1.0960 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TrN+I+G partition = 010020 -lnL = 1054.3085 K = 16 freqA = 0.4221 freqC = 0.1529 freqG = 0.2043 freqT = 0.2207 R(a) [AC] = 1.0000 R(b) [AG] = 0.5081 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 1.0933 R(f) [GT] = 1.0000 p-inv = 0.2720 gamma shape = 0.0100 Model = TPM1 partition = 012210 -lnL = 1115.2090 K = 11 R(a) [AC] = 1.0000 R(b) [AG] = 0.6908 R(c) [AT] = 0.9971 R(d) [CG] = 0.9971 R(e) [CT] = 0.6908 R(f) [GT] = 1.0000 Model = TPM1+I partition = 012210 -lnL = 1113.4794 K = 12 R(a) [AC] = 1.0000 R(b) [AG] = 0.6902 R(c) [AT] = 0.9965 R(d) [CG] = 0.9965 R(e) [CT] = 0.6902 R(f) [GT] = 1.0000 p-inv = 0.3000 Model = TPM1+G partition = 012210 -lnL = 1106.0854 K = 12 R(a) [AC] = 1.0000 R(b) [AG] = 0.6849 R(c) [AT] = 0.9842 R(d) [CG] = 0.9842 R(e) [CT] = 0.6849 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TPM1+I+G partition = 012210 -lnL = 1104.8628 K = 13 R(a) [AC] = 1.0000 R(b) [AG] = 0.6840 R(c) [AT] = 0.9813 R(d) [CG] = 0.9813 R(e) [CT] = 0.6840 R(f) [GT] = 1.0000 p-inv = 0.2780 gamma shape = 0.0110 Model = TPM1uf partition = 012210 -lnL = 1064.9670 K = 14 freqA = 0.4209 freqC = 0.1541 freqG = 0.2027 freqT = 0.2224 R(a) [AC] = 1.0000 R(b) [AG] = 0.6316 R(c) [AT] = 0.8718 R(d) [CG] = 0.8718 R(e) [CT] = 0.6316 R(f) [GT] = 1.0000 Model = TPM1uf+I partition = 012210 -lnL = 1063.2547 K = 15 freqA = 0.4214 freqC = 0.1538 freqG = 0.2026 freqT = 0.2222 R(a) [AC] = 1.0000 R(b) [AG] = 0.6313 R(c) [AT] = 0.8718 R(d) [CG] = 0.8718 R(e) [CT] = 0.6313 R(f) [GT] = 1.0000 p-inv = 0.2970 Model = TPM1uf+G partition = 012210 -lnL = 1055.9633 K = 15 freqA = 0.4205 freqC = 0.1542 freqG = 0.2029 freqT = 0.2225 R(a) [AC] = 1.0000 R(b) [AG] = 0.6242 R(c) [AT] = 0.8608 R(d) [CG] = 0.8608 R(e) [CT] = 0.6242 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TPM1uf+I+G partition = 012210 -lnL = 1054.7937 K = 16 freqA = 0.4209 freqC = 0.1540 freqG = 0.2028 freqT = 0.2223 R(a) [AC] = 1.0000 R(b) [AG] = 0.6244 R(c) [AT] = 0.8607 R(d) [CG] = 0.8607 R(e) [CT] = 0.6244 R(f) [GT] = 1.0000 p-inv = 0.2740 gamma shape = 0.0110 Model = TPM2 partition = 010212 -lnL = 1115.1681 K = 11 R(a) [AC] = 0.8940 R(b) [AG] = 0.6469 R(c) [AT] = 0.8940 R(d) [CG] = 1.0000 R(e) [CT] = 0.6469 R(f) [GT] = 1.0000 Model = TPM2+I partition = 010212 -lnL = 1113.4693 K = 12 R(a) [AC] = 0.9443 R(b) [AG] = 0.6687 R(c) [AT] = 0.9443 R(d) [CG] = 1.0000 R(e) [CT] = 0.6687 R(f) [GT] = 1.0000 p-inv = 0.2960 Model = TPM2+G partition = 010212 -lnL = 1106.0467 K = 12 R(a) [AC] = 0.8876 R(b) [AG] = 0.6435 R(c) [AT] = 0.8876 R(d) [CG] = 1.0000 R(e) [CT] = 0.6435 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TPM2+I+G partition = 010212 -lnL = 1104.8147 K = 13 R(a) [AC] = 0.9538 R(b) [AG] = 0.6716 R(c) [AT] = 0.9538 R(d) [CG] = 1.0000 R(e) [CT] = 0.6716 R(f) [GT] = 1.0000 p-inv = 0.2820 gamma shape = 0.0110 Model = TPM2uf partition = 010212 -lnL = 1064.4579 K = 14 freqA = 0.4229 freqC = 0.1543 freqG = 0.2007 freqT = 0.2222 R(a) [AC] = 0.6464 R(b) [AG] = 0.5162 R(c) [AT] = 0.6464 R(d) [CG] = 1.0000 R(e) [CT] = 0.5162 R(f) [GT] = 1.0000 Model = TPM2uf+I partition = 010212 -lnL = 1062.7429 K = 15 freqA = 0.4236 freqC = 0.1541 freqG = 0.2004 freqT = 0.2219 R(a) [AC] = 0.6444 R(b) [AG] = 0.5154 R(c) [AT] = 0.6444 R(d) [CG] = 1.0000 R(e) [CT] = 0.5154 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = TPM2uf+G partition = 010212 -lnL = 1055.4684 K = 15 freqA = 0.4225 freqC = 0.1544 freqG = 0.2009 freqT = 0.2222 R(a) [AC] = 0.6353 R(b) [AG] = 0.5096 R(c) [AT] = 0.6353 R(d) [CG] = 1.0000 R(e) [CT] = 0.5096 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TPM2uf+I+G partition = 010212 -lnL = 1054.3109 K = 16 freqA = 0.4231 freqC = 0.1543 freqG = 0.2006 freqT = 0.2221 R(a) [AC] = 0.6363 R(b) [AG] = 0.5101 R(c) [AT] = 0.6363 R(d) [CG] = 1.0000 R(e) [CT] = 0.5101 R(f) [GT] = 1.0000 p-inv = 0.2720 gamma shape = 0.0110 Model = TPM3 partition = 012012 -lnL = 1115.2084 K = 11 R(a) [AC] = 0.9863 R(b) [AG] = 0.6870 R(c) [AT] = 1.0000 R(d) [CG] = 0.9863 R(e) [CT] = 0.6870 R(f) [GT] = 1.0000 Model = TPM3+I partition = 012012 -lnL = 1113.4762 K = 12 R(a) [AC] = 0.9687 R(b) [AG] = 0.6816 R(c) [AT] = 1.0000 R(d) [CG] = 0.9687 R(e) [CT] = 0.6816 R(f) [GT] = 1.0000 p-inv = 0.3000 Model = TPM3+G partition = 012012 -lnL = 1106.0862 K = 12 R(a) [AC] = 1.0016 R(b) [AG] = 0.6909 R(c) [AT] = 1.0000 R(d) [CG] = 1.0016 R(e) [CT] = 0.6909 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TPM3+I+G partition = 012012 -lnL = 1104.8631 K = 13 R(a) [AC] = 0.9829 R(b) [AG] = 0.6848 R(c) [AT] = 1.0000 R(d) [CG] = 0.9829 R(e) [CT] = 0.6848 R(f) [GT] = 1.0000 p-inv = 0.2780 gamma shape = 0.0110 Model = TPM3uf partition = 012012 -lnL = 1064.8545 K = 14 freqA = 0.4208 freqC = 0.1531 freqG = 0.2028 freqT = 0.2234 R(a) [AC] = 1.2673 R(b) [AG] = 0.7516 R(c) [AT] = 1.0000 R(d) [CG] = 1.2673 R(e) [CT] = 0.7516 R(f) [GT] = 1.0000 Model = TPM3uf+I partition = 012012 -lnL = 1063.1428 K = 15 freqA = 0.4212 freqC = 0.1528 freqG = 0.2027 freqT = 0.2233 R(a) [AC] = 1.2690 R(b) [AG] = 0.7515 R(c) [AT] = 1.0000 R(d) [CG] = 1.2690 R(e) [CT] = 0.7515 R(f) [GT] = 1.0000 p-inv = 0.2970 Model = TPM3uf+G partition = 012012 -lnL = 1055.8414 K = 15 freqA = 0.4204 freqC = 0.1532 freqG = 0.2030 freqT = 0.2234 R(a) [AC] = 1.2993 R(b) [AG] = 0.7553 R(c) [AT] = 1.0000 R(d) [CG] = 1.2993 R(e) [CT] = 0.7553 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TPM3uf+I+G partition = 012012 -lnL = 1054.6733 K = 16 freqA = 0.4208 freqC = 0.1529 freqG = 0.2030 freqT = 0.2234 R(a) [AC] = 1.2978 R(b) [AG] = 0.7551 R(c) [AT] = 1.0000 R(d) [CG] = 1.2978 R(e) [CT] = 0.7551 R(f) [GT] = 1.0000 p-inv = 0.2730 gamma shape = 0.0100 Model = TIM1ef partition = 012230 -lnL = 1115.1348 K = 12 R(a) [AC] = 1.0000 R(b) [AG] = 0.6203 R(c) [AT] = 0.9971 R(d) [CG] = 0.9971 R(e) [CT] = 0.8043 R(f) [GT] = 1.0000 Model = TIM1ef+I partition = 012230 -lnL = 1113.4381 K = 13 R(a) [AC] = 1.0000 R(b) [AG] = 0.6357 R(c) [AT] = 0.9963 R(d) [CG] = 0.9963 R(e) [CT] = 0.7729 R(f) [GT] = 1.0000 p-inv = 0.2950 Model = TIM1ef+G partition = 012230 -lnL = 1106.0043 K = 13 R(a) [AC] = 1.0000 R(b) [AG] = 0.6088 R(c) [AT] = 0.9835 R(d) [CG] = 0.9835 R(e) [CT] = 0.8097 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TIM1ef+I+G partition = 012230 -lnL = 1104.7820 K = 14 R(a) [AC] = 1.0000 R(b) [AG] = 0.6271 R(c) [AT] = 0.9811 R(d) [CG] = 0.9811 R(e) [CT] = 0.7701 R(f) [GT] = 1.0000 p-inv = 0.2800 gamma shape = 0.0110 Model = TIM1 partition = 012230 -lnL = 1064.4392 K = 15 freqA = 0.4221 freqC = 0.1529 freqG = 0.2038 freqT = 0.2212 R(a) [AC] = 1.0000 R(b) [AG] = 0.4871 R(c) [AT] = 0.8713 R(d) [CG] = 0.8713 R(e) [CT] = 0.9963 R(f) [GT] = 1.0000 Model = TIM1+I partition = 012230 -lnL = 1062.7237 K = 16 freqA = 0.4227 freqC = 0.1525 freqG = 0.2039 freqT = 0.2209 R(a) [AC] = 1.0000 R(b) [AG] = 0.4850 R(c) [AT] = 0.8715 R(d) [CG] = 0.8715 R(e) [CT] = 0.9984 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = TIM1+G partition = 012230 -lnL = 1055.4008 K = 16 freqA = 0.4217 freqC = 0.1529 freqG = 0.2041 freqT = 0.2212 R(a) [AC] = 1.0000 R(b) [AG] = 0.4701 R(c) [AT] = 0.8589 R(d) [CG] = 0.8589 R(e) [CT] = 1.0154 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TIM1+I+G partition = 012230 -lnL = 1054.2374 K = 17 freqA = 0.4223 freqC = 0.1527 freqG = 0.2041 freqT = 0.2209 R(a) [AC] = 1.0000 R(b) [AG] = 0.4703 R(c) [AT] = 0.8591 R(d) [CG] = 0.8591 R(e) [CT] = 1.0141 R(f) [GT] = 1.0000 p-inv = 0.2720 gamma shape = 0.0100 Model = TIM2ef partition = 010232 -lnL = 1115.0964 K = 12 R(a) [AC] = 0.8966 R(b) [AG] = 0.5834 R(c) [AT] = 0.8966 R(d) [CG] = 1.0000 R(e) [CT] = 0.7531 R(f) [GT] = 1.0000 Model = TIM2ef+I partition = 010232 -lnL = 1113.4278 K = 13 R(a) [AC] = 0.9438 R(b) [AG] = 0.6154 R(c) [AT] = 0.9438 R(d) [CG] = 1.0000 R(e) [CT] = 0.7494 R(f) [GT] = 1.0000 p-inv = 0.2920 Model = TIM2ef+G partition = 010232 -lnL = 1105.9646 K = 13 R(a) [AC] = 0.8872 R(b) [AG] = 0.5715 R(c) [AT] = 0.8872 R(d) [CG] = 1.0000 R(e) [CT] = 0.7615 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TIM2ef+I+G partition = 010232 -lnL = 1104.7365 K = 14 R(a) [AC] = 0.9520 R(b) [AG] = 0.6147 R(c) [AT] = 0.9520 R(d) [CG] = 1.0000 R(e) [CT] = 0.7562 R(f) [GT] = 1.0000 p-inv = 0.2830 gamma shape = 0.0110 Model = TIM2 partition = 010232 -lnL = 1063.9345 K = 15 freqA = 0.4240 freqC = 0.1531 freqG = 0.2018 freqT = 0.2210 R(a) [AC] = 0.6482 R(b) [AG] = 0.3994 R(c) [AT] = 0.6482 R(d) [CG] = 1.0000 R(e) [CT] = 0.8138 R(f) [GT] = 1.0000 Model = TIM2+I partition = 010232 -lnL = 1062.2186 K = 16 freqA = 0.4249 freqC = 0.1528 freqG = 0.2017 freqT = 0.2206 R(a) [AC] = 0.6464 R(b) [AG] = 0.3978 R(c) [AT] = 0.6464 R(d) [CG] = 1.0000 R(e) [CT] = 0.8137 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = TIM2+G partition = 010232 -lnL = 1054.9223 K = 16 freqA = 0.4236 freqC = 0.1532 freqG = 0.2022 freqT = 0.2210 R(a) [AC] = 0.6412 R(b) [AG] = 0.3875 R(c) [AT] = 0.6412 R(d) [CG] = 1.0000 R(e) [CT] = 0.8283 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TIM2+I+G partition = 010232 -lnL = 1053.7735 K = 17 freqA = 0.4244 freqC = 0.1529 freqG = 0.2020 freqT = 0.2207 R(a) [AC] = 0.6427 R(b) [AG] = 0.3883 R(c) [AT] = 0.6427 R(d) [CG] = 1.0000 R(e) [CT] = 0.8281 R(f) [GT] = 1.0000 p-inv = 0.2710 gamma shape = 0.0100 Model = TIM3ef partition = 012032 -lnL = 1115.1341 K = 12 R(a) [AC] = 0.9855 R(b) [AG] = 0.6170 R(c) [AT] = 1.0000 R(d) [CG] = 0.9855 R(e) [CT] = 0.8001 R(f) [GT] = 1.0000 Model = TIM3ef+I partition = 012032 -lnL = 1113.4349 K = 13 R(a) [AC] = 0.9689 R(b) [AG] = 0.6274 R(c) [AT] = 1.0000 R(d) [CG] = 0.9689 R(e) [CT] = 0.7630 R(f) [GT] = 1.0000 p-inv = 0.2960 Model = TIM3ef+G partition = 012032 -lnL = 1106.0051 K = 13 R(a) [AC] = 1.0015 R(b) [AG] = 0.6143 R(c) [AT] = 1.0000 R(d) [CG] = 1.0015 R(e) [CT] = 0.8170 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TIM3ef+I+G partition = 012032 -lnL = 1104.7825 K = 14 R(a) [AC] = 0.9830 R(b) [AG] = 0.6280 R(c) [AT] = 1.0000 R(d) [CG] = 0.9830 R(e) [CT] = 0.7711 R(f) [GT] = 1.0000 p-inv = 0.2800 gamma shape = 0.0100 Model = TIM3 partition = 012032 -lnL = 1064.3246 K = 15 freqA = 0.4219 freqC = 0.1519 freqG = 0.2040 freqT = 0.2222 R(a) [AC] = 1.2690 R(b) [AG] = 0.5792 R(c) [AT] = 1.0000 R(d) [CG] = 1.2690 R(e) [CT] = 1.1876 R(f) [GT] = 1.0000 Model = TIM3+I partition = 012032 -lnL = 1062.6090 K = 16 freqA = 0.4226 freqC = 0.1515 freqG = 0.2040 freqT = 0.2220 R(a) [AC] = 1.2720 R(b) [AG] = 0.5787 R(c) [AT] = 1.0000 R(d) [CG] = 1.2720 R(e) [CT] = 1.1911 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = TIM3+G partition = 012032 -lnL = 1055.2704 K = 16 freqA = 0.4216 freqC = 0.1519 freqG = 0.2042 freqT = 0.2223 R(a) [AC] = 1.3119 R(b) [AG] = 0.5708 R(c) [AT] = 1.0000 R(d) [CG] = 1.3119 R(e) [CT] = 1.2407 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TIM3+I+G partition = 012032 -lnL = 1054.1076 K = 17 freqA = 0.4222 freqC = 0.1515 freqG = 0.2043 freqT = 0.2221 R(a) [AC] = 1.3099 R(b) [AG] = 0.5706 R(c) [AT] = 1.0000 R(d) [CG] = 1.3099 R(e) [CT] = 1.2383 R(f) [GT] = 1.0000 p-inv = 0.2720 gamma shape = 0.0110 Model = TVMef partition = 012314 -lnL = 1115.1675 K = 13 R(a) [AC] = 0.8818 R(b) [AG] = 0.6437 R(c) [AT] = 0.8958 R(d) [CG] = 0.9902 R(e) [CT] = 0.6437 R(f) [GT] = 1.0000 Model = TVMef+I partition = 012314 -lnL = 1113.4661 K = 14 R(a) [AC] = 0.9153 R(b) [AG] = 0.6571 R(c) [AT] = 0.9401 R(d) [CG] = 0.9639 R(e) [CT] = 0.6571 R(f) [GT] = 1.0000 p-inv = 0.2970 Model = TVMef+G partition = 012314 -lnL = 1106.0465 K = 14 R(a) [AC] = 0.8899 R(b) [AG] = 0.6415 R(c) [AT] = 0.8818 R(d) [CG] = 0.9941 R(e) [CT] = 0.6415 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TVMef+I+G partition = 012314 -lnL = 1104.8121 K = 15 R(a) [AC] = 0.9361 R(b) [AG] = 0.6591 R(c) [AT] = 0.9368 R(d) [CG] = 0.9616 R(e) [CT] = 0.6591 R(f) [GT] = 1.0000 p-inv = 0.2830 gamma shape = 0.0110 Model = TVM partition = 012314 -lnL = 1064.2834 K = 16 freqA = 0.4229 freqC = 0.1531 freqG = 0.2007 freqT = 0.2234 R(a) [AC] = 0.8171 R(b) [AG] = 0.5641 R(c) [AT] = 0.6299 R(d) [CG] = 1.2268 R(e) [CT] = 0.5641 R(f) [GT] = 1.0000 Model = TVM+I partition = 012314 -lnL = 1062.5693 K = 17 freqA = 0.4236 freqC = 0.1528 freqG = 0.2004 freqT = 0.2233 R(a) [AC] = 0.8151 R(b) [AG] = 0.5625 R(c) [AT] = 0.6273 R(d) [CG] = 1.2269 R(e) [CT] = 0.5625 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = TVM+G partition = 012314 -lnL = 1055.2762 K = 17 freqA = 0.4225 freqC = 0.1532 freqG = 0.2009 freqT = 0.2235 R(a) [AC] = 0.8222 R(b) [AG] = 0.5591 R(c) [AT] = 0.6126 R(d) [CG] = 1.2360 R(e) [CT] = 0.5591 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = TVM+I+G partition = 012314 -lnL = 1054.1197 K = 18 freqA = 0.4231 freqC = 0.1529 freqG = 0.2006 freqT = 0.2234 R(a) [AC] = 0.8215 R(b) [AG] = 0.5585 R(c) [AT] = 0.6120 R(d) [CG] = 1.2314 R(e) [CT] = 0.5585 R(f) [GT] = 1.0000 p-inv = 0.2720 gamma shape = 0.0100 Model = SYM partition = 012345 -lnL = 1115.0957 K = 14 R(a) [AC] = 0.8840 R(b) [AG] = 0.5801 R(c) [AT] = 0.8986 R(d) [CG] = 0.9890 R(e) [CT] = 0.7489 R(f) [GT] = 1.0000 Model = SYM+I partition = 012345 -lnL = 1113.4246 K = 15 R(a) [AC] = 0.9147 R(b) [AG] = 0.6049 R(c) [AT] = 0.9394 R(d) [CG] = 0.9645 R(e) [CT] = 0.7362 R(f) [GT] = 1.0000 p-inv = 0.2920 Model = SYM+G partition = 012345 -lnL = 1105.9644 K = 15 R(a) [AC] = 0.8887 R(b) [AG] = 0.5695 R(c) [AT] = 0.8805 R(d) [CG] = 0.9938 R(e) [CT] = 0.7589 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = SYM+I+G partition = 012345 -lnL = 1104.7340 K = 16 R(a) [AC] = 0.9344 R(b) [AG] = 0.6036 R(c) [AT] = 0.9351 R(d) [CG] = 0.9621 R(e) [CT] = 0.7426 R(f) [GT] = 1.0000 p-inv = 0.2840 gamma shape = 0.0100 Model = GTR partition = 012345 -lnL = 1063.7577 K = 17 freqA = 0.4240 freqC = 0.1520 freqG = 0.2018 freqT = 0.2222 R(a) [AC] = 0.8200 R(b) [AG] = 0.4362 R(c) [AT] = 0.6313 R(d) [CG] = 1.2290 R(e) [CT] = 0.8900 R(f) [GT] = 1.0000 Model = GTR+I partition = 012345 -lnL = 1062.0417 K = 18 freqA = 0.4249 freqC = 0.1515 freqG = 0.2017 freqT = 0.2220 R(a) [AC] = 0.8195 R(b) [AG] = 0.4345 R(c) [AT] = 0.6291 R(d) [CG] = 1.2301 R(e) [CT] = 0.8917 R(f) [GT] = 1.0000 p-inv = 0.2980 Model = GTR+G partition = 012345 -lnL = 1054.7203 K = 18 freqA = 0.4236 freqC = 0.1519 freqG = 0.2022 freqT = 0.2223 R(a) [AC] = 0.8365 R(b) [AG] = 0.4257 R(c) [AT] = 0.6175 R(d) [CG] = 1.2481 R(e) [CT] = 0.9174 R(f) [GT] = 1.0000 gamma shape = 0.0230 Model = GTR+I+G partition = 012345 -lnL = 1053.5709 K = 19 freqA = 0.4244 freqC = 0.1515 freqG = 0.2020 freqT = 0.2221 R(a) [AC] = 0.8390 R(b) [AG] = 0.4261 R(c) [AT] = 0.6182 R(d) [CG] = 1.2449 R(e) [CT] = 0.9164 R(f) [GT] = 1.0000 p-inv = 0.2710 gamma shape = 0.0110 Unconstrained -lnL = 986.87328 Number of patterns found = 28 Computation of likelihood scores completed. It took 00h:00:00:04. --------------------------------------------------------------- * * * AKAIKE INFORMATION CRITERION (AIC) * * * --------------------------------------------------------------- Model selected: Model = F81+I+G partition = 000000 -lnL = 1055.3705 K = 14 freqA = 0.4206 freqC = 0.1546 freqG = 0.2021 freqT = 0.2228 p-inv = 0.2740 gamma shape = 0.0100 -- PAUP* Commands Block: If you want to load the selected model and associated estimates in PAUP*, attach the next block of commands after the data in your PAUP file: [! Likelihood settings from best-fit model (F81+I+G) selected by AIC with jModeltest 2.1.6 v20140903 on Wed Sep 17 07:31:19 PDT 2014] BEGIN PAUP; Lset base=(0.4206 0.1546 0.2021 ) nst=1 rates=gamma shape=0.0100 ncat=4 pinvar=0.2740; END; -- Tree for the best AIC model = (((P4:0.00695639,(P6:0.00587334,P1:0.00000006):0.00184123):0.00190371,P5:0.00805688):0.00930078,P3:0.01292532,P2:0.00479644); * AIC MODEL SELECTION : Selection uncertainty Model -lnL K AIC delta weight cumWeight uDelta -------------------------------------------------------------------------------------- F81+I+G 1055.37046 14 2138.740920 0.000000 0.150886 0.150886 110.9944 F81+G 1056.54525 13 2139.090500 0.349580 0.126689 0.277575 111.3439 HKY+I+G 1054.86274 15 2139.725480 0.984560 0.092226 0.369801 111.9789 HKY+G 1056.03207 14 2140.064140 1.323220 0.077860 0.447661 112.3176 TrN+I+G 1054.30851 16 2140.617020 1.876100 0.059055 0.506716 112.8705 TPM2uf+I+G 1054.31091 16 2140.621820 1.880900 0.058914 0.565630 112.8753 TPM2uf+G 1055.46838 15 2140.936760 2.195840 0.050330 0.615960 113.1902 TrN+G 1055.47105 15 2140.942100 2.201180 0.050196 0.666156 113.1955 TPM3uf+I+G 1054.67331 16 2141.346620 2.605700 0.041004 0.707160 113.6001 TIM2+I+G 1053.77348 17 2141.546960 2.806040 0.037096 0.744256 113.8004 TPM1uf+I+G 1054.79365 16 2141.587300 2.846380 0.036355 0.780611 113.8407 TPM3uf+G 1055.84138 15 2141.682760 2.941840 0.034661 0.815272 113.9362 TIM2+G 1054.92226 16 2141.844520 3.103600 0.031968 0.847239 114.0980 TPM1uf+G 1055.96332 15 2141.926640 3.185720 0.030682 0.877921 114.1801 TIM3+I+G 1054.10758 17 2142.215160 3.474240 0.026560 0.904481 114.4686 TIM1+I+G 1054.23739 17 2142.474780 3.733860 0.023327 0.927808 114.7282 TIM3+G 1055.27036 16 2142.540720 3.799800 0.022570 0.950378 114.7942 TIM1+G 1055.40084 16 2142.801680 4.060760 0.019809 0.970187 115.0551 TVM+I+G 1054.11967 18 2144.239340 5.498420 0.009653 0.979840 116.4928 TVM+G 1055.27620 17 2144.552400 5.811480 0.008255 0.988095 116.8058 GTR+I+G 1053.57092 19 2145.141840 6.400920 0.006148 0.994242 117.3953 GTR+G 1054.72028 18 2145.440560 6.699640 0.005295 0.999537 117.6940 F81+I 1063.84069 13 2153.681380 14.940460 8.60e-005 0.999623 125.9348 HKY+I 1063.31470 14 2154.629400 15.888480 5.35e-005 0.999677 126.8828 F81 1065.55370 12 2155.107400 16.366480 4.21e-005 0.999719 127.3608 TPM2uf+I 1062.74293 15 2155.485860 16.744940 3.49e-005 0.999754 127.7393 TrN+I 1062.78408 15 2155.568160 16.827240 3.35e-005 0.999787 127.8216 HKY 1065.02723 13 2156.054460 17.313540 2.62e-005 0.999813 128.3079 TPM3uf+I 1063.14285 15 2156.285700 17.544780 2.34e-005 0.999837 128.5391 TIM2+I 1062.21861 16 2156.437220 17.696300 2.17e-005 0.999858 128.6907 TPM1uf+I 1063.25469 15 2156.509380 17.768460 2.09e-005 0.999879 128.7628 TPM2uf 1064.45794 14 2156.915880 18.174960 1.71e-005 0.999896 129.1693 TrN 1064.49967 14 2156.999340 18.258420 1.64e-005 0.999913 129.2528 TIM3+I 1062.60896 16 2157.217920 18.477000 1.47e-005 0.999927 129.4714 TIM1+I 1062.72369 16 2157.447380 18.706460 1.31e-005 0.999941 129.7008 TPM3uf 1064.85445 14 2157.708900 18.967980 1.15e-005 0.999952 129.9623 TIM2 1063.93452 15 2157.869040 19.128120 1.06e-005 0.999963 130.1225 TPM1uf 1064.96702 14 2157.934040 19.193120 1.03e-005 0.999973 130.1875 TIM3 1064.32461 15 2158.649220 19.908300 7.17e-006 0.999980 130.9027 TIM1 1064.43916 15 2158.878320 20.137400 6.40e-006 0.999986 131.1318 TVM+I 1062.56932 17 2159.138640 20.397720 5.61e-006 0.999992 131.3921 GTR+I 1062.04173 18 2160.083460 21.342540 3.50e-006 0.999996 132.3369 TVM 1064.28338 16 2160.566760 21.825840 2.75e-006 0.999998 132.8202 GTR 1063.75769 17 2161.515380 22.774460 1.71e-006 1.000000 133.7688 JC+I+G 1105.31786 11 2232.635720 93.894800 6.16e-022 1.000000 204.8892 JC+G 1106.54549 10 2233.090980 94.350060 4.91e-022 1.000000 205.3444 K80+I+G 1104.86395 12 2233.727900 94.986980 3.57e-022 1.000000 205.9813 K80+G 1106.08621 11 2234.172420 95.431500 2.86e-022 1.000000 206.4259 TrNef+I+G 1104.78317 13 2235.566340 96.825420 1.42e-022 1.000000 207.8198 TPM2+I+G 1104.81467 13 2235.629340 96.888420 1.38e-022 1.000000 207.8828 TPM1+I+G 1104.86279 13 2235.725580 96.984660 1.31e-022 1.000000 207.9790 TPM3+I+G 1104.86307 13 2235.726140 96.985220 1.31e-022 1.000000 207.9796 TrNef+G 1106.00515 12 2236.010300 97.269380 1.14e-022 1.000000 208.2637 TPM2+G 1106.04673 12 2236.093460 97.352540 1.09e-022 1.000000 208.3469 TPM1+G 1106.08538 12 2236.170760 97.429840 1.05e-022 1.000000 208.4242 TPM3+G 1106.08620 12 2236.172400 97.431480 1.05e-022 1.000000 208.4258 TIM2ef+I+G 1104.73654 14 2237.473080 98.732160 5.49e-023 1.000000 209.7265 TIM1ef+I+G 1104.78204 14 2237.564080 98.823160 5.24e-023 1.000000 209.8175 TIM3ef+I+G 1104.78247 14 2237.564940 98.824020 5.24e-023 1.000000 209.8184 TIM2ef+G 1105.96459 13 2237.929180 99.188260 4.37e-023 1.000000 210.1826 TIM1ef+G 1106.00429 13 2238.008580 99.267660 4.20e-023 1.000000 210.2620 TIM3ef+G 1106.00514 13 2238.010280 99.269360 4.19e-023 1.000000 210.2637 TVMef+I+G 1104.81214 15 2239.624280 100.883360 1.87e-023 1.000000 211.8777 TVMef+G 1106.04653 14 2240.093060 101.352140 1.48e-023 1.000000 212.3465 SYM+I+G 1104.73399 16 2241.467980 102.727060 7.44e-024 1.000000 213.7214 SYM+G 1105.96438 15 2241.928760 103.187840 5.91e-024 1.000000 214.1822 JC+I 1113.95428 10 2247.908560 109.167640 2.97e-025 1.000000 220.1620 K80+I 1113.47946 11 2248.958920 110.218000 1.76e-025 1.000000 221.2124 JC 1115.68456 9 2249.369120 110.628200 1.43e-025 1.000000 221.6226 K80 1115.20898 10 2250.417960 111.677040 8.48e-026 1.000000 222.6714 TrNef+I 1113.43812 12 2250.876240 112.135320 6.74e-026 1.000000 223.1297 TPM2+I 1113.46932 12 2250.938640 112.197720 6.53e-026 1.000000 223.1921 TPM3+I 1113.47623 12 2250.952460 112.211540 6.49e-026 1.000000 223.2059 TPM1+I 1113.47942 12 2250.958840 112.217920 6.47e-026 1.000000 223.2123 TrNef 1115.13480 11 2252.269600 113.528680 3.36e-026 1.000000 224.5230 TPM2 1115.16811 11 2252.336220 113.595300 3.25e-026 1.000000 224.5897 TPM3 1115.20838 11 2252.416760 113.675840 3.12e-026 1.000000 224.6702 TPM1 1115.20896 11 2252.417920 113.677000 3.12e-026 1.000000 224.6714 TIM2ef+I 1113.42777 13 2252.855540 114.114620 2.51e-026 1.000000 225.1090 TIM3ef+I 1113.43493 13 2252.869860 114.128940 2.49e-026 1.000000 225.1233 TIM1ef+I 1113.43808 13 2252.876160 114.135240 2.48e-026 1.000000 225.1296 TIM2ef 1115.09640 12 2254.192800 115.451880 1.28e-026 1.000000 226.4462 TIM3ef 1115.13411 12 2254.268220 115.527300 1.24e-026 1.000000 226.5217 TIM1ef 1115.13477 12 2254.269540 115.528620 1.24e-026 1.000000 226.5230 TVMef+I 1113.46614 14 2254.932280 116.191360 8.87e-027 1.000000 227.1857 TVMef 1115.16752 13 2256.335040 117.594120 4.40e-027 1.000000 228.5885 SYM+I 1113.42463 15 2256.849260 118.108340 3.40e-027 1.000000 229.1027 SYM 1115.09572 14 2258.191440 119.450520 1.74e-027 1.000000 230.4449 -------------------------------------------------------------------------------------- -lnL: negative log likelihod K: number of estimated parameters AIC: Akaike Information Criterion delta: AIC difference weight: AIC weight cumWeight: cumulative AIC weight * AIC MODEL SELECTION : Confidence interval There are 88 models in the 100% confidence interval: [ F81+I+G F81+G HKY+I+G HKY+G TrN+I+G TPM2uf+I+G TPM2uf+G TrN+G TPM3uf+I+G TIM2+I+G TPM1uf+I+G TPM3uf+G TIM2+G TPM1uf+G TIM3+I+G TIM1+I+G TIM3+G TIM1+G TVM+I+G TVM+G GTR+I+G GTR+G F81+I HKY+I F81 TPM2uf+I TrN+I HKY TPM3uf+I TIM2+I TPM1uf+I TPM2uf TrN TIM3+I TIM1+I TPM3uf TIM2 TPM1uf TIM3 TIM1 TVM+I GTR+I TVM GTR JC+I+G JC+G K80+I+G K80+G TrNef+I+G TPM2+I+G TPM1+I+G TPM3+I+G TrNef+G TPM2+G TPM1+G TPM3+G TIM2ef+I+G TIM1ef+I+G TIM3ef+I+G TIM2ef+G TIM1ef+G TIM3ef+G TVMef+I+G TVMef+G SYM+I+G SYM+G JC+I K80+I JC K80 TrNef+I TPM2+I TPM3+I TPM1+I TrNef TPM2 TPM3 TPM1 TIM2ef+I TIM3ef+I TIM1ef+I TIM2ef TIM3ef TIM1ef TVMef+I TVMef SYM+I SYM ] * AIC MODEL SELECTION : Parameter importance Parameter Importance ---------------------- fA 1.0000 fC 1.0000 fG 1.0000 fT 1.0000 kappa 0.1702 titv 0.1702 rAC 0.3326 rAG 0.5521 rAT 0.3180 rCG 0.2644 rCT 0.5521 rGT 0.5521 pinv(I) 0.0003 alpha(G) 0.4583 pinv(IG) 0.5412 alpha(IG) 0.5412 ---------------------- Values have been rounded. (I): considers only +I models. (G): considers only +G models. (IG): considers only +I+G models. * AIC MODEL SELECTION : Best Model's command line phyml -i /tmp/jmodeltest4579695484136556156.phy -d nt -n 1 -b 0 --run_id F81+I+G -m 000000 -f m -v e -c 4 -a e --no_memory_check -u /tmp/jmodeltest7971412443020107151.tree -o lr --------------------------------------------------------------- * * * MODEL AVERAGED PHYLOGENY * * * --------------------------------------------------------------- Selection criterion: . . . . AIC Confidence interval: . . . . 1.00 Consensus type:. . . . . . . 50% majority rule Using 88 models in the 1.00 confidence interval = F81+I+G F81+G HKY+I+G HKY+G TrN+I+G TPM2uf+I+G TPM2uf+G TrN+G TPM3uf+I+G TIM2+I+G TPM1uf+I+G TPM3uf+G TIM2+G TPM1uf+G TIM3+I+G TIM1+I+G TIM3+G TIM1+G TVM+I+G TVM+G GTR+I+G GTR+G F81+I HKY+I F81 TPM2uf+I TrN+I HKY TPM3uf+I TIM2+I TPM1uf+I TPM2uf TrN TIM3+I TIM1+I TPM3uf TIM2 TPM1uf TIM3 TIM1 TVM+I GTR+I TVM GTR JC+I+G JC+G K80+I+G K80+G TrNef+I+G TPM2+I+G TPM1+I+G TPM3+I+G TrNef+G TPM2+G TPM1+G TPM3+G TIM2ef+I+G TIM1ef+I+G TIM3ef+I+G TIM2ef+G TIM1ef+G TIM3ef+G TVMef+I+G TVMef+G SYM+I+G SYM+G JC+I K80+I JC K80 TrNef+I TPM2+I TPM3+I TPM1+I TrNef TPM2 TPM3 TPM1 TIM2ef+I TIM3ef+I TIM1ef+I TIM2ef TIM3ef TIM1ef TVMef+I TVMef SYM+I SYM Species in order: 1. P4 2. P6 3. P1 4. P5 5. P3 6. P2 Bipartitions included in the consensus tree 123456 ****** ( 1.0 ) ****-- ( 1.0 ) ***--- ( 1.0 ) -**--- ( 1.0 ) +-6 P1 +--7 | +-----------5 P6 +---8 | +-------------4 P4 +------------------9 | +----------------3 P5 | +---------2 P2 | +--------------------------1 P3 (P3:0.012965,P2:0.004842,(P5:0.008080,(P4:0.006994,(P6:0.005924,P1:0.000000)1.00:0.001868)1.00:0.001914)1.00:0.009412); Note: this tree is unrooted. Branch lengths are the expected number of substitutions per site. Labels next to parentheses represent phylogenetic uncertainty due to model selection (see documentation) --------------------------------------------------------------- * * * CORRECTED AKAIKE INFORMATION CRITERION (AICc) * * * --------------------------------------------------------------- Sample size: 631.0 Model selected: Model = F81+I+G partition = 000000 -lnL = 1055.3705 K = 14 freqA = 0.4206 freqC = 0.1546 freqG = 0.2021 freqT = 0.2228 p-inv = 0.2740 gamma shape = 0.0100 -- PAUP* Commands Block: If you want to load the selected model and associated estimates in PAUP*, attach the next block of commands after the data in your PAUP file: [! Likelihood settings from best-fit model (F81+I+G) selected by AICc with jModeltest 2.1.6 v20140903 on Wed Sep 17 07:31:19 PDT 2014] BEGIN PAUP; Lset base=(0.4206 0.1546 0.2021 ) nst=1 rates=gamma shape=0.0100 ncat=4 pinvar=0.2740; END; -- Tree for the best AICc model = (((P4:0.00695639,(P6:0.00587334,P1:0.00000006):0.00184123):0.00190371,P5:0.00805688):0.00930078,P3:0.01292532,P2:0.00479644); * AICc MODEL SELECTION : Selection uncertainty Model -lnL K AICc delta weight cumWeight uDelta -------------------------------------------------------------------------------------- F81+I+G 1055.37046 14 2139.422738 0.000000 0.158998 0.158998 109.1687 F81+G 1056.54525 13 2139.680451 0.257713 0.139775 0.298773 109.4264 HKY+I+G 1054.86274 15 2140.505968 1.083230 0.092506 0.391279 110.2519 HKY+G 1056.03207 14 2140.745958 1.323220 0.082046 0.473325 110.4919 TrN+I+G 1054.30851 16 2141.503013 2.080275 0.056191 0.529516 111.2490 TPM2uf+I+G 1054.31091 16 2141.507813 2.085075 0.056056 0.585572 111.2538 TPM2uf+G 1055.46838 15 2141.717248 2.294510 0.050483 0.636055 111.4632 TrN+G 1055.47105 15 2141.722588 2.299850 0.050348 0.686404 111.4686 TPM3uf+I+G 1054.67331 16 2142.232613 2.809875 0.039015 0.725419 111.9786 TPM3uf+G 1055.84138 15 2142.463248 3.040510 0.034766 0.760185 112.2092 TPM1uf+I+G 1054.79365 16 2142.473293 3.050555 0.034592 0.794776 112.2193 TIM2+I+G 1053.77348 17 2142.545329 3.122590 0.033368 0.828144 112.2913 TPM1uf+G 1055.96332 15 2142.707128 3.284390 0.030775 0.858919 112.4531 TIM2+G 1054.92226 16 2142.730513 3.307775 0.030417 0.889336 112.4765 TIM3+I+G 1054.10758 17 2143.213529 3.790790 0.023891 0.913227 112.9595 TIM3+G 1055.27036 16 2143.426713 4.003975 0.021475 0.934702 113.1727 TIM1+I+G 1054.23739 17 2143.473149 4.050410 0.020982 0.955685 113.2191 TIM1+G 1055.40084 16 2143.687673 4.264935 0.018848 0.974533 113.4337 TVM+I+G 1054.11967 18 2145.356987 5.934249 0.008181 0.982714 115.1030 TVM+G 1055.27620 17 2145.550769 6.128030 0.007425 0.990139 115.2967 GTR+I+G 1053.57092 19 2146.385703 6.962964 0.004891 0.995030 116.1317 GTR+G 1054.72028 18 2146.558207 7.135469 0.004487 0.999517 116.3042 F81+I 1063.84069 13 2154.271331 14.848593 9.49e-005 0.999612 124.0173 HKY+I 1063.31470 14 2155.311218 15.888480 5.64e-005 0.999668 125.0572 F81 1065.55370 12 2155.612254 16.189516 4.85e-005 0.999717 125.3582 TPM2uf+I 1062.74293 15 2156.266348 16.843610 3.50e-005 0.999751 126.0123 TrN+I 1062.78408 15 2156.348648 16.925910 3.36e-005 0.999785 126.0946 HKY 1065.02723 13 2156.644411 17.221673 2.90e-005 0.999814 126.3904 TPM3uf+I 1063.14285 15 2157.066188 17.643450 2.35e-005 0.999837 126.8122 TPM1uf+I 1063.25469 15 2157.289868 17.867130 2.10e-005 0.999858 127.0358 TIM2+I 1062.21861 16 2157.323213 17.900475 2.06e-005 0.999879 127.0692 TPM2uf 1064.45794 14 2157.597698 18.174960 1.80e-005 0.999897 127.3437 TrN 1064.49967 14 2157.681158 18.258420 1.72e-005 0.999914 127.4271 TIM3+I 1062.60896 16 2158.103913 18.681175 1.40e-005 0.999928 127.8499 TIM1+I 1062.72369 16 2158.333373 18.910635 1.24e-005 0.999941 128.0794 TPM3uf 1064.85445 14 2158.390718 18.967980 1.21e-005 0.999953 128.1367 TPM1uf 1064.96702 14 2158.615858 19.193120 1.08e-005 0.999964 128.3618 TIM2 1063.93452 15 2158.649528 19.226790 1.06e-005 0.999974 128.3955 TIM3 1064.32461 15 2159.429708 20.006970 7.19e-006 0.999981 129.1757 TIM1 1064.43916 15 2159.658808 20.236070 6.41e-006 0.999988 129.4048 TVM+I 1062.56932 17 2160.137009 20.714270 5.05e-006 0.999993 129.8830 GTR+I 1062.04173 18 2161.201107 21.778369 2.97e-006 0.999996 130.9471 TVM 1064.28338 16 2161.452753 22.030015 2.62e-006 0.999998 131.1987 GTR 1063.75769 17 2162.513749 23.091010 1.54e-006 1.000000 132.2597 JC+I+G 1105.31786 11 2233.062214 93.639476 7.38e-022 1.000000 202.8082 JC+G 1106.54549 10 2233.445819 94.023081 6.09e-022 1.000000 203.1918 K80+I+G 1104.86395 12 2234.232754 94.810016 4.11e-022 1.000000 203.9787 K80+G 1106.08621 11 2234.598914 95.176176 3.42e-022 1.000000 204.3449 TrNef+I+G 1104.78317 13 2236.156291 96.733553 1.57e-022 1.000000 205.9023 TPM2+I+G 1104.81467 13 2236.219291 96.796553 1.52e-022 1.000000 205.9653 TPM1+I+G 1104.86279 13 2236.315531 96.892793 1.45e-022 1.000000 206.0615 TPM3+I+G 1104.86307 13 2236.316091 96.893353 1.45e-022 1.000000 206.0621 TrNef+G 1106.00515 12 2236.515154 97.092416 1.31e-022 1.000000 206.2611 TPM2+G 1106.04673 12 2236.598314 97.175576 1.26e-022 1.000000 206.3443 TPM1+G 1106.08538 12 2236.675614 97.252876 1.21e-022 1.000000 206.4216 TPM3+G 1106.08620 12 2236.677254 97.254516 1.21e-022 1.000000 206.4232 TIM2ef+I+G 1104.73654 14 2238.154898 98.732160 5.78e-023 1.000000 207.9009 TIM1ef+I+G 1104.78204 14 2238.245898 98.823160 5.52e-023 1.000000 207.9919 TIM3ef+I+G 1104.78247 14 2238.246758 98.824020 5.52e-023 1.000000 207.9927 TIM2ef+G 1105.96459 13 2238.519131 99.096393 4.82e-023 1.000000 208.2651 TIM1ef+G 1106.00429 13 2238.598531 99.175793 4.63e-023 1.000000 208.3445 TIM3ef+G 1106.00514 13 2238.600231 99.177493 4.63e-023 1.000000 208.3462 TVMef+I+G 1104.81214 15 2240.404768 100.982030 1.88e-023 1.000000 210.1507 TVMef+G 1106.04653 14 2240.774878 101.352140 1.56e-023 1.000000 210.5209 SYM+I+G 1104.73399 16 2242.353973 102.931235 7.08e-024 1.000000 212.1000 SYM+G 1105.96438 15 2242.709248 103.286510 5.93e-024 1.000000 212.4552 JC+I 1113.95428 10 2248.263399 108.840661 3.69e-025 1.000000 218.0094 K80+I 1113.47946 11 2249.385414 109.962676 2.11e-025 1.000000 219.1314 JC 1115.68456 9 2249.658975 110.236237 1.84e-025 1.000000 219.4050 K80 1115.20898 10 2250.772799 111.350061 1.05e-025 1.000000 220.5188 TrNef+I 1113.43812 12 2251.381094 111.958356 7.76e-026 1.000000 221.1271 TPM2+I 1113.46932 12 2251.443494 112.020756 7.52e-026 1.000000 221.1895 TPM3+I 1113.47623 12 2251.457314 112.034576 7.47e-026 1.000000 221.2033 TPM1+I 1113.47942 12 2251.463694 112.040956 7.45e-026 1.000000 221.2097 TrNef 1115.13480 11 2252.696094 113.273356 4.02e-026 1.000000 222.4421 TPM2 1115.16811 11 2252.762714 113.339976 3.89e-026 1.000000 222.5087 TPM3 1115.20838 11 2252.843254 113.420516 3.74e-026 1.000000 222.5892 TPM1 1115.20896 11 2252.844414 113.421676 3.73e-026 1.000000 222.5904 TIM2ef+I 1113.42777 13 2253.445491 114.022753 2.76e-026 1.000000 223.1915 TIM3ef+I 1113.43493 13 2253.459811 114.037073 2.75e-026 1.000000 223.2058 TIM1ef+I 1113.43808 13 2253.466111 114.043373 2.74e-026 1.000000 223.2121 TIM2ef 1115.09640 12 2254.697654 115.274916 1.48e-026 1.000000 224.4436 TIM3ef 1115.13411 12 2254.773074 115.350336 1.42e-026 1.000000 224.5191 TIM1ef 1115.13477 12 2254.774394 115.351656 1.42e-026 1.000000 224.5204 TVMef+I 1113.46614 14 2255.614098 116.191360 9.35e-027 1.000000 225.3601 TVMef 1115.16752 13 2256.924991 117.502253 4.85e-027 1.000000 226.6710 SYM+I 1113.42463 15 2257.629748 118.207010 3.41e-027 1.000000 227.3757 SYM 1115.09572 14 2258.873258 119.450520 1.83e-027 1.000000 228.6192 -------------------------------------------------------------------------------------- -lnL: negative log likelihod K: number of estimated parameters AICc: Corrected Akaike Information Criterion delta: AICc difference weight: AICc weight cumWeight: cumulative AICc weight * AICc MODEL SELECTION : Confidence interval There are 88 models in the 100% confidence interval: [ F81+I+G F81+G HKY+I+G HKY+G TrN+I+G TPM2uf+I+G TPM2uf+G TrN+G TPM3uf+I+G TPM3uf+G TPM1uf+I+G TIM2+I+G TPM1uf+G TIM2+G TIM3+I+G TIM3+G TIM1+I+G TIM1+G TVM+I+G TVM+G GTR+I+G GTR+G F81+I HKY+I F81 TPM2uf+I TrN+I HKY TPM3uf+I TPM1uf+I TIM2+I TPM2uf TrN TIM3+I TIM1+I TPM3uf TPM1uf TIM2 TIM3 TIM1 TVM+I GTR+I TVM GTR JC+I+G JC+G K80+I+G K80+G TrNef+I+G TPM2+I+G TPM1+I+G TPM3+I+G TrNef+G TPM2+G TPM1+G TPM3+G TIM2ef+I+G TIM1ef+I+G TIM3ef+I+G TIM2ef+G TIM1ef+G TIM3ef+G TVMef+I+G TVMef+G SYM+I+G SYM+G JC+I K80+I JC K80 TrNef+I TPM2+I TPM3+I TPM1+I TrNef TPM2 TPM3 TPM1 TIM2ef+I TIM3ef+I TIM1ef+I TIM2ef TIM3ef TIM1ef TVMef+I TVMef SYM+I SYM ] * AICc MODEL SELECTION : Parameter importance Parameter Importance ---------------------- fA 1.0000 fC 1.0000 fG 1.0000 fT 1.0000 kappa 0.1746 titv 0.1746 rAC 0.3146 rAG 0.5264 rAT 0.3007 rCG 0.2494 rCT 0.5264 rGT 0.5264 pinv(I) 0.0003 alpha(G) 0.4708 pinv(IG) 0.5287 alpha(IG) 0.5287 ---------------------- Values have been rounded. (I): considers only +I models. (G): considers only +G models. (IG): considers only +I+G models. * AICc MODEL SELECTION : Best Model's command line phyml -i /tmp/jmodeltest4579695484136556156.phy -d nt -n 1 -b 0 --run_id F81+I+G -m 000000 -f m -v e -c 4 -a e --no_memory_check -u /tmp/jmodeltest7971412443020107151.tree -o lr --------------------------------------------------------------- * * * MODEL AVERAGED PHYLOGENY * * * --------------------------------------------------------------- Selection criterion: . . . . AICc Confidence interval: . . . . 1.00 Consensus type:. . . . . . . 50% majority rule Using 88 models in the 1.00 confidence interval = F81+I+G F81+G HKY+I+G HKY+G TrN+I+G TPM2uf+I+G TPM2uf+G TrN+G TPM3uf+I+G TPM3uf+G TPM1uf+I+G TIM2+I+G TPM1uf+G TIM2+G TIM3+I+G TIM3+G TIM1+I+G TIM1+G TVM+I+G TVM+G GTR+I+G GTR+G F81+I HKY+I F81 TPM2uf+I TrN+I HKY TPM3uf+I TPM1uf+I TIM2+I TPM2uf TrN TIM3+I TIM1+I TPM3uf TPM1uf TIM2 TIM3 TIM1 TVM+I GTR+I TVM GTR JC+I+G JC+G K80+I+G K80+G TrNef+I+G TPM2+I+G TPM1+I+G TPM3+I+G TrNef+G TPM2+G TPM1+G TPM3+G TIM2ef+I+G TIM1ef+I+G TIM3ef+I+G TIM2ef+G TIM1ef+G TIM3ef+G TVMef+I+G TVMef+G SYM+I+G SYM+G JC+I K80+I JC K80 TrNef+I TPM2+I TPM3+I TPM1+I TrNef TPM2 TPM3 TPM1 TIM2ef+I TIM3ef+I TIM1ef+I TIM2ef TIM3ef TIM1ef TVMef+I TVMef SYM+I SYM Species in order: 1. P4 2. P6 3. P1 4. P5 5. P3 6. P2 Bipartitions included in the consensus tree 123456 ****** ( 1.0 ) ****-- ( 1.0 ) ***--- ( 1.0 ) -**--- ( 1.0 ) +-6 P1 +--7 | +-----------5 P6 +---8 | +-------------4 P4 +------------------9 | +----------------3 P5 | +---------2 P2 | +--------------------------1 P3 (P3:0.012965,P2:0.004842,(P5:0.008080,(P4:0.006994,(P6:0.005924,P1:0.000000)1.00:0.001868)1.00:0.001918)1.00:0.009412); Note: this tree is unrooted. Branch lengths are the expected number of substitutions per site. Labels next to parentheses represent phylogenetic uncertainty due to model selection (see documentation) --------------------------------------------------------------- * * * BAYESIAN INFORMATION CRITERION (BIC) * * * --------------------------------------------------------------- Sample size: 631.0 Model selected: Model = F81+G partition = 000000 -lnL = 1056.5452 K = 13 freqA = 0.4203 freqC = 0.1547 freqG = 0.2022 freqT = 0.2229 gamma shape = 0.0230 -- PAUP* Commands Block: If you want to load the selected model and associated estimates in PAUP*, attach the next block of commands after the data in your PAUP file: [! Likelihood settings from best-fit model (F81+G) selected by BIC with jModeltest 2.1.6 v20140903 on Wed Sep 17 07:31:19 PDT 2014] BEGIN PAUP; Lset base=(0.4203 0.1547 0.2022 ) nst=1 rates=gamma shape=0.0230 ncat=4 pinvar=0; END; -- Tree for the best BIC model = (((P4:0.00794016,(P6:0.00668997,P1:0.00000017):0.00209170):0.00204577,P5:0.00927680):0.01072876,P3:0.01498511,P2:0.00533876); * BIC MODEL SELECTION : Selection uncertainty Model -lnL K BIC delta weight cumWeight uDelta -------------------------------------------------------------------------------------- F81+G 1056.54525 13 2196.905476 0.000000 0.815587 0.815587 49.0817 F81+I+G 1055.37046 14 2201.003202 4.097726 0.105114 0.920701 53.1794 HKY+G 1056.03207 14 2202.326422 5.420946 0.054241 0.974942 54.5026 HKY+I+G 1054.86274 15 2206.435068 9.529592 0.006953 0.981894 58.6112 TPM2uf+G 1055.46838 15 2207.646348 10.740872 0.003794 0.985689 59.8225 TrN+G 1055.47105 15 2207.651688 10.746212 0.003784 0.989473 59.8279 TPM3uf+G 1055.84138 15 2208.392348 11.486872 0.002613 0.992086 60.5685 F81 1065.55370 12 2208.475070 11.569594 0.002507 0.994593 60.6513 TPM1uf+G 1055.96332 15 2208.636228 11.730752 0.002313 0.996906 60.8124 F81+I 1063.84069 13 2211.496356 14.590880 0.000553 0.997459 63.6725 TrN+I+G 1054.30851 16 2211.773914 14.868438 0.000482 0.997941 63.9501 TPM2uf+I+G 1054.31091 16 2211.778714 14.873238 0.000481 0.998421 63.9549 TPM3uf+I+G 1054.67331 16 2212.503514 15.598038 0.000335 0.998756 64.6797 TPM1uf+I+G 1054.79365 16 2212.744194 15.838718 0.000297 0.999053 64.9204 TIM2+G 1054.92226 16 2213.001414 16.095938 0.000261 0.999313 65.1776 TIM3+G 1055.27036 16 2213.697614 16.792138 0.000184 0.999497 65.8738 HKY 1065.02723 13 2213.869436 16.963960 0.000169 0.999666 66.0456 TIM1+G 1055.40084 16 2213.958574 17.053098 0.000162 0.999828 66.1348 HKY+I 1063.31470 14 2216.891682 19.986206 3.73e-005 0.999865 69.0679 TIM2+I+G 1053.77348 17 2217.151160 20.245683 3.27e-005 0.999898 69.3273 TIM3+I+G 1054.10758 17 2217.819360 20.913883 2.34e-005 0.999921 69.9955 TIM1+I+G 1054.23739 17 2218.078980 21.173503 2.06e-005 0.999942 70.2552 TPM2uf 1064.45794 14 2219.178162 22.272686 1.19e-005 0.999954 71.3543 TrN 1064.49967 14 2219.261622 22.356146 1.14e-005 0.999965 71.4378 TPM3uf 1064.85445 14 2219.971182 23.065706 7.99e-006 0.999973 72.1474 TVM+G 1055.27620 17 2220.156600 23.251123 7.29e-006 0.999981 72.3328 TPM1uf 1064.96702 14 2220.196322 23.290846 7.14e-006 0.999988 72.3725 TPM2uf+I 1062.74293 15 2222.195448 25.289972 2.63e-006 0.999990 74.3716 TrN+I 1062.78408 15 2222.277748 25.372272 2.52e-006 0.999993 74.4539 TPM3uf+I 1063.14285 15 2222.995288 26.089812 1.76e-006 0.999995 75.1715 TPM1uf+I 1063.25469 15 2223.218968 26.313492 1.58e-006 0.999996 75.3951 TVM+I+G 1054.11967 18 2224.290846 27.385369 9.22e-007 0.999997 76.4670 TIM2 1063.93452 15 2224.578628 27.673152 7.99e-007 0.999998 76.7548 TIM3 1064.32461 15 2225.358808 28.453332 5.41e-007 0.999999 77.5350 GTR+G 1054.72028 18 2225.492066 28.586589 5.06e-007 0.999999 77.6682 TIM1 1064.43916 15 2225.587908 28.682432 4.82e-007 1.000000 77.7641 TIM2+I 1062.21861 16 2227.594114 30.688638 1.77e-007 1.000000 79.7703 TIM3+I 1062.60896 16 2228.374814 31.469338 1.20e-007 1.000000 80.5510 TIM1+I 1062.72369 16 2228.604274 31.698798 1.07e-007 1.000000 80.7805 GTR+I+G 1053.57092 19 2229.640651 32.735175 6.36e-008 1.000000 81.8168 TVM 1064.28338 16 2231.723654 34.818178 2.24e-008 1.000000 83.8998 TVM+I 1062.56932 17 2234.742840 37.837363 4.96e-009 1.000000 86.9190 GTR 1063.75769 17 2237.119580 40.214103 1.51e-009 1.000000 89.2958 GTR+I 1062.04173 18 2240.134966 43.229489 3.34e-010 1.000000 92.3111 JC+G 1106.54549 10 2277.564039 80.658562 2.49e-018 1.000000 129.7402 JC+I+G 1105.31786 11 2281.556084 84.650608 3.39e-019 1.000000 133.7323 K80+G 1106.08621 11 2283.092784 86.187308 1.57e-019 1.000000 135.2690 K80+I+G 1104.86395 12 2287.095570 90.190094 2.12e-020 1.000000 139.2718 TrNef+G 1106.00515 12 2289.377970 92.472494 6.78e-021 1.000000 141.5542 JC 1115.68456 9 2289.394873 92.489397 6.72e-021 1.000000 141.5711 TPM2+G 1106.04673 12 2289.461130 92.555654 6.51e-021 1.000000 141.6373 TPM1+G 1106.08538 12 2289.538430 92.632954 6.26e-021 1.000000 141.7146 TPM3+G 1106.08620 12 2289.540070 92.634594 6.25e-021 1.000000 141.7163 JC+I 1113.95428 10 2292.381619 95.476142 1.51e-021 1.000000 144.5578 TrNef+I+G 1104.78317 13 2293.381316 96.475840 9.16e-022 1.000000 145.5575 TPM2+I+G 1104.81467 13 2293.444316 96.538840 8.88e-022 1.000000 145.6205 TPM1+I+G 1104.86279 13 2293.540556 96.635080 8.46e-022 1.000000 145.7167 TPM3+I+G 1104.86307 13 2293.541116 96.635640 8.46e-022 1.000000 145.7173 K80 1115.20898 10 2294.891019 97.985542 4.31e-022 1.000000 147.0672 TIM2ef+G 1105.96459 13 2295.744156 98.838680 2.81e-022 1.000000 147.9203 TIM1ef+G 1106.00429 13 2295.823556 98.918080 2.70e-022 1.000000 147.9997 TIM3ef+G 1106.00514 13 2295.825256 98.919780 2.70e-022 1.000000 148.0014 K80+I 1113.47946 11 2297.879284 100.973808 9.67e-023 1.000000 150.0555 TIM2ef+I+G 1104.73654 14 2299.735362 102.829886 3.82e-023 1.000000 151.9115 TIM1ef+I+G 1104.78204 14 2299.826362 102.920886 3.65e-023 1.000000 152.0025 TIM3ef+I+G 1104.78247 14 2299.827222 102.921746 3.65e-023 1.000000 152.0034 TrNef 1115.13480 11 2301.189964 104.284488 1.85e-023 1.000000 153.3661 TPM2 1115.16811 11 2301.256584 104.351108 1.79e-023 1.000000 153.4328 TPM3 1115.20838 11 2301.337124 104.431648 1.72e-023 1.000000 153.5133 TPM1 1115.20896 11 2301.338284 104.432808 1.71e-023 1.000000 153.5145 TVMef+G 1106.04653 14 2302.355342 105.449866 1.03e-023 1.000000 154.5315 TrNef+I 1113.43812 12 2304.243910 107.338434 4.01e-024 1.000000 156.4201 TPM2+I 1113.46932 12 2304.306310 107.400834 3.89e-024 1.000000 156.4825 TPM3+I 1113.47623 12 2304.320130 107.414654 3.86e-024 1.000000 156.4963 TPM1+I 1113.47942 12 2304.326510 107.421034 3.85e-024 1.000000 156.5027 TVMef+I+G 1104.81214 15 2306.333868 109.428392 1.41e-024 1.000000 158.5100 TIM2ef 1115.09640 12 2307.560470 110.654994 7.64e-025 1.000000 159.7367 TIM3ef 1115.13411 12 2307.635890 110.730414 7.36e-025 1.000000 159.8121 TIM1ef 1115.13477 12 2307.637210 110.731734 7.35e-025 1.000000 159.8134 SYM+G 1105.96438 15 2308.638348 111.732872 4.46e-025 1.000000 160.8145 TIM2ef+I 1113.42777 13 2310.670516 113.765040 1.61e-025 1.000000 162.8467 TIM3ef+I 1113.43493 13 2310.684836 113.779360 1.60e-025 1.000000 162.8610 TIM1ef+I 1113.43808 13 2310.691136 113.785660 1.60e-025 1.000000 162.8673 SYM+I+G 1104.73399 16 2312.624874 115.719398 6.07e-026 1.000000 164.8011 TVMef 1115.16752 13 2314.150016 117.244540 2.83e-026 1.000000 166.3262 TVMef+I 1113.46614 14 2317.194562 120.289086 6.18e-027 1.000000 169.3707 SYM 1115.09572 14 2320.453722 123.548246 1.21e-027 1.000000 172.6299 SYM+I 1113.42463 15 2323.558848 126.653372 2.56e-028 1.000000 175.7350 -------------------------------------------------------------------------------------- -lnL: negative log likelihod K: number of estimated parameters BIC: Bayesian Information Criterion delta: BIC difference weight: BIC weight cumWeight: cumulative BIC weight * BIC MODEL SELECTION : Confidence interval There are 88 models in the 100% confidence interval: [ F81+G F81+I+G HKY+G HKY+I+G TPM2uf+G TrN+G TPM3uf+G F81 TPM1uf+G F81+I TrN+I+G TPM2uf+I+G TPM3uf+I+G TPM1uf+I+G TIM2+G TIM3+G HKY TIM1+G HKY+I TIM2+I+G TIM3+I+G TIM1+I+G TPM2uf TrN TPM3uf TVM+G TPM1uf TPM2uf+I TrN+I TPM3uf+I TPM1uf+I TVM+I+G TIM2 TIM3 GTR+G TIM1 TIM2+I TIM3+I TIM1+I GTR+I+G TVM TVM+I GTR GTR+I JC+G JC+I+G K80+G K80+I+G TrNef+G JC TPM2+G TPM1+G TPM3+G JC+I TrNef+I+G TPM2+I+G TPM1+I+G TPM3+I+G K80 TIM2ef+G TIM1ef+G TIM3ef+G K80+I TIM2ef+I+G TIM1ef+I+G TIM3ef+I+G TrNef TPM2 TPM3 TPM1 TVMef+G TrNef+I TPM2+I TPM3+I TPM1+I TVMef+I+G TIM2ef TIM3ef TIM1ef SYM+G TIM2ef+I TIM3ef+I TIM1ef+I SYM+I+G TVMef TVMef+I SYM SYM+I ] * BIC MODEL SELECTION : Parameter importance Parameter Importance ---------------------- fA 1.0000 fC 1.0000 fG 1.0000 fT 1.0000 kappa 0.0614 titv 0.0614 rAC 0.0078 rAG 0.0148 rAT 0.0074 rCG 0.0060 rCT 0.0148 rGT 0.0148 pinv(I) 0.0006 alpha(G) 0.8829 pinv(IG) 0.1137 alpha(IG) 0.1137 ---------------------- Values have been rounded. (I): considers only +I models. (G): considers only +G models. (IG): considers only +I+G models. * BIC MODEL SELECTION : Best Model's command line phyml -i /tmp/jmodeltest4579695484136556156.phy -d nt -n 1 -b 0 --run_id F81+G -m 000000 -f m -c 4 -a e --no_memory_check -u /tmp/jmodeltest7971412443020107151.tree -o lr --------------------------------------------------------------- * * * MODEL AVERAGED PHYLOGENY * * * --------------------------------------------------------------- Selection criterion: . . . . BIC Confidence interval: . . . . 1.00 Consensus type:. . . . . . . 50% majority rule Using 88 models in the 1.00 confidence interval = F81+G F81+I+G HKY+G HKY+I+G TPM2uf+G TrN+G TPM3uf+G F81 TPM1uf+G F81+I TrN+I+G TPM2uf+I+G TPM3uf+I+G TPM1uf+I+G TIM2+G TIM3+G HKY TIM1+G HKY+I TIM2+I+G TIM3+I+G TIM1+I+G TPM2uf TrN TPM3uf TVM+G TPM1uf TPM2uf+I TrN+I TPM3uf+I TPM1uf+I TVM+I+G TIM2 TIM3 GTR+G TIM1 TIM2+I TIM3+I TIM1+I GTR+I+G TVM TVM+I GTR GTR+I JC+G JC+I+G K80+G K80+I+G TrNef+G JC TPM2+G TPM1+G TPM3+G JC+I TrNef+I+G TPM2+I+G TPM1+I+G TPM3+I+G K80 TIM2ef+G TIM1ef+G TIM3ef+G K80+I TIM2ef+I+G TIM1ef+I+G TIM3ef+I+G TrNef TPM2 TPM3 TPM1 TVMef+G TrNef+I TPM2+I TPM3+I TPM1+I TVMef+I+G TIM2ef TIM3ef TIM1ef SYM+G TIM2ef+I TIM3ef+I TIM1ef+I SYM+I+G TVMef TVMef+I SYM SYM+I Species in order: 1. P4 2. P6 3. P1 4. P5 5. P3 6. P2 Bipartitions included in the consensus tree 123456 ****** ( 1.0 ) ****-- ( 1.0 ) ***--- ( 1.0 ) -**--- ( 1.0 ) +-6 P1 +---7 | +-------------5 P6 +---8 | +---------------4 P4 +---------------------9 | +------------------3 P5 | +----------2 P2 | +------------------------------1 P3 (P3:0.014985,P2:0.005339,(P5:0.009277,(P4:0.007940,(P6:0.006690,P1:0.000000)1.00:0.002092)1.00:0.002046)1.00:0.010729); Note: this tree is unrooted. Branch lengths are the expected number of substitutions per site. Labels next to parentheses represent phylogenetic uncertainty due to model selection (see documentation) --------------------------------------------------------------- * * * DECISION THEORY PERFORMANCE-BASED SELECTION (DT) * * * --------------------------------------------------------------- Sample size: 631.0 Model selected: Model = F81+G partition = 000000 -lnL = 1056.5452 K = 13 freqA = 0.4203 freqC = 0.1547 freqG = 0.2022 freqT = 0.2229 gamma shape = 0.0230 -- PAUP* Commands Block: If you want to load the selected model and associated estimates in PAUP*, attach the next block of commands after the data in your PAUP file: [! Likelihood settings from best-fit model (F81+G) selected by DT with jModeltest 2.1.6 v20140903 on Wed Sep 17 07:31:19 PDT 2014] BEGIN PAUP; Lset base=(0.4203 0.1547 0.2022 ) nst=1 rates=gamma shape=0.0230 ncat=4 pinvar=0; END; -- Tree for the best DT model = (((P4:0.00794016,(P6:0.00668997,P1:0.00000017):0.00209170):0.00204577,P5:0.00927680):0.01072876,P3:0.01498511,P2:0.00533876); * DT MODEL SELECTION : Selection uncertainty Model -lnL K DT delta weight cumWeight ------------------------------------------------------------------------- F81+G 1056.54525 13 0.000380 0.000000 0.049306 0.049306 TPM1uf+G 1055.96332 15 0.000430 0.000050 0.043566 0.092872 HKY+G 1056.03207 14 0.000447 0.000067 0.041921 0.134793 TPM3uf+G 1055.84138 15 0.000463 0.000083 0.040491 0.175284 TVM+G 1055.27620 17 0.000476 0.000096 0.039346 0.214630 TPM2uf+G 1055.46838 15 0.000497 0.000117 0.037670 0.252300 TrN+G 1055.47105 15 0.000552 0.000172 0.033943 0.286243 TIM2+G 1054.92226 16 0.000552 0.000172 0.033921 0.320164 TIM1+G 1055.40084 16 0.000571 0.000191 0.032783 0.352947 GTR+G 1054.72028 18 0.000606 0.000226 0.030896 0.383842 K80+G 1106.08621 11 0.000615 0.000235 0.030450 0.414293 TPM3+G 1106.08620 12 0.000616 0.000236 0.030414 0.444706 TPM1+G 1106.08538 12 0.000619 0.000239 0.030262 0.474969 TIM3+G 1055.27036 16 0.000633 0.000254 0.029570 0.504538 JC+G 1106.54549 10 0.000666 0.000286 0.028114 0.532653 TPM2+G 1106.04673 12 0.000730 0.000350 0.025663 0.558315 TVMef+G 1106.04653 14 0.000731 0.000351 0.025618 0.583933 TrNef+G 1106.00515 12 0.000766 0.000386 0.024451 0.608385 TIM3ef+G 1106.00514 13 0.000767 0.000387 0.024422 0.632807 TIM1ef+G 1106.00429 13 0.000770 0.000390 0.024315 0.657122 TIM2ef+G 1105.96459 13 0.000940 0.000560 0.019921 0.677043 SYM+G 1105.96438 15 0.000943 0.000563 0.019855 0.696898 TIM2ef+I+G 1104.73654 14 0.002595 0.002215 0.007219 0.704117 SYM+I+G 1104.73399 16 0.002608 0.002228 0.007181 0.711298 GTR+I+G 1053.57092 19 0.002655 0.002275 0.007056 0.718354 TrNef+I+G 1104.78317 13 0.002678 0.002298 0.006993 0.725347 TIM3+I+G 1054.10758 17 0.002678 0.002298 0.006993 0.732340 TIM1ef+I+G 1104.78204 14 0.002678 0.002299 0.006993 0.739333 TIM3ef+I+G 1104.78247 14 0.002686 0.002306 0.006972 0.746305 TIM2+I+G 1053.77348 17 0.002695 0.002315 0.006951 0.753256 TIM1+I+G 1054.23739 17 0.002705 0.002325 0.006924 0.760180 TVM+I+G 1054.11967 18 0.002709 0.002329 0.006913 0.767093 TrN+I+G 1054.30851 16 0.002718 0.002338 0.006891 0.773984 TPM2+I+G 1104.81467 13 0.002724 0.002345 0.006875 0.780858 TVMef+I+G 1104.81214 15 0.002736 0.002356 0.006846 0.787704 TPM3uf+I+G 1054.67331 16 0.002738 0.002358 0.006842 0.794546 TPM2uf+I+G 1054.31091 16 0.002747 0.002367 0.006819 0.801365 TPM1uf+I+G 1054.79365 16 0.002761 0.002381 0.006784 0.808149 F81+I+G 1055.37046 14 0.002772 0.002392 0.006757 0.814906 HKY+I+G 1054.86274 15 0.002776 0.002396 0.006747 0.821653 JC+I+G 1105.31786 11 0.002807 0.002427 0.006673 0.828326 TPM1+I+G 1104.86279 13 0.002808 0.002428 0.006670 0.834996 K80+I+G 1104.86395 12 0.002808 0.002428 0.006669 0.841665 TPM3+I+G 1104.86307 13 0.002819 0.002439 0.006645 0.848310 JC 1115.68456 9 0.004674 0.004294 0.004007 0.852317 F81 1065.55370 12 0.004674 0.004294 0.004007 0.856325 K80 1115.20898 10 0.004674 0.004294 0.004007 0.860332 HKY 1065.02723 13 0.004674 0.004294 0.004007 0.864339 TrNef 1115.13480 11 0.004674 0.004294 0.004007 0.868346 TrN 1064.49967 14 0.004674 0.004294 0.004007 0.872353 TPM1 1115.20896 11 0.004674 0.004294 0.004007 0.876360 TPM1uf 1064.96702 14 0.004674 0.004294 0.004007 0.880367 TPM2 1115.16811 11 0.004674 0.004294 0.004007 0.884375 TPM2uf 1064.45794 14 0.004674 0.004294 0.004007 0.888382 TPM3 1115.20838 11 0.004674 0.004294 0.004007 0.892389 TPM3uf 1064.85445 14 0.004674 0.004294 0.004007 0.896396 TIM1ef 1115.13477 12 0.004674 0.004294 0.004007 0.900403 TIM1 1064.43916 15 0.004674 0.004294 0.004007 0.904410 TIM2ef 1115.09640 12 0.004674 0.004294 0.004007 0.908417 TIM2 1063.93452 15 0.004674 0.004294 0.004007 0.912425 TIM3ef 1115.13411 12 0.004674 0.004294 0.004007 0.916432 TIM3 1064.32461 15 0.004674 0.004294 0.004007 0.920439 TVMef 1115.16752 13 0.004674 0.004294 0.004007 0.924446 TVM 1064.28338 16 0.004674 0.004294 0.004007 0.928453 SYM 1115.09572 14 0.004674 0.004294 0.004007 0.932460 GTR 1063.75769 17 0.004674 0.004294 0.004007 0.936467 TIM2ef+I 1113.42777 13 0.006375 0.005995 0.002938 0.939405 SYM+I 1113.42463 15 0.006386 0.006006 0.002933 0.942338 TrNef+I 1113.43812 12 0.006443 0.006064 0.002907 0.945245 TIM1ef+I 1113.43808 13 0.006444 0.006064 0.002907 0.948152 TIM3ef+I 1113.43493 13 0.006457 0.006077 0.002901 0.951053 TPM2+I 1113.46932 12 0.006467 0.006087 0.002896 0.953949 TVMef+I 1113.46614 14 0.006482 0.006102 0.002890 0.956838 TPM3uf+I 1063.14285 15 0.006489 0.006109 0.002886 0.959725 TPM1uf+I 1063.25469 15 0.006493 0.006113 0.002885 0.962609 HKY+I 1063.31470 14 0.006495 0.006115 0.002884 0.965493 F81+I 1063.84069 13 0.006496 0.006116 0.002883 0.968376 TVM+I 1062.56932 17 0.006496 0.006116 0.002883 0.971259 TIM3+I 1062.60896 16 0.006498 0.006118 0.002882 0.974142 GTR+I 1062.04173 18 0.006500 0.006120 0.002882 0.977023 TIM1+I 1062.72369 16 0.006500 0.006120 0.002881 0.979905 TrN+I 1062.78408 15 0.006502 0.006122 0.002880 0.982785 TPM2uf+I 1062.74293 15 0.006502 0.006123 0.002880 0.985665 TIM2+I 1062.21861 16 0.006503 0.006123 0.002880 0.988546 TPM1+I 1113.47942 12 0.006537 0.006157 0.002865 0.991411 K80+I 1113.47946 11 0.006537 0.006157 0.002865 0.994276 JC+I 1113.95428 10 0.006538 0.006158 0.002865 0.997141 TPM3+I 1113.47623 12 0.006551 0.006171 0.002859 1.000000 ------------------------------------------------------------------------- -lnL:t negative log likelihod K: number of estimated parameters DT: decision theory performance-based score delta: DT difference weight: DT weight* (calculated using 1/DT) cumWeight: cumulative DT weight * DT MODEL SELECTION : Confidence interval There are 88 models in the 100% confidence interval: [ F81+G TPM1uf+G HKY+G TPM3uf+G TVM+G TPM2uf+G TrN+G TIM2+G TIM1+G GTR+G K80+G TPM3+G TPM1+G TIM3+G JC+G TPM2+G TVMef+G TrNef+G TIM3ef+G TIM1ef+G TIM2ef+G SYM+G TIM2ef+I+G SYM+I+G GTR+I+G TrNef+I+G TIM3+I+G TIM1ef+I+G TIM3ef+I+G TIM2+I+G TIM1+I+G TVM+I+G TrN+I+G TPM2+I+G TVMef+I+G TPM3uf+I+G TPM2uf+I+G TPM1uf+I+G F81+I+G HKY+I+G JC+I+G TPM1+I+G K80+I+G TPM3+I+G JC F81 K80 HKY TrNef TrN TPM1 TPM1uf TPM2 TPM2uf TPM3 TPM3uf TIM1ef TIM1 TIM2ef TIM2 TIM3ef TIM3 TVMef TVM SYM GTR TIM2ef+I SYM+I TrNef+I TIM1ef+I TIM3ef+I TPM2+I TVMef+I TPM3uf+I TPM1uf+I HKY+I F81+I TVM+I TIM3+I GTR+I TIM1+I TrN+I TPM2uf+I TIM2+I TPM1+I K80+I JC+I TPM3+I ] * DT MODEL SELECTION : Parameter importance Parameter Importance ---------------------- fA 0.5649 fC 0.5649 fG 0.5649 fT 0.5649 kappa 0.0995 titv 0.0995 rAC 0.5239 rAG 0.7958 rAT 0.5299 rCG 0.5371 rCT 0.7958 rGT 0.7958 pinv(I) 0.0635 alpha(G) 0.6969 pinv(IG) 0.1514 alpha(IG) 0.1514 ---------------------- Values have been rounded. (I): considers only +I models. (G): considers only +G models. (IG): considers only +I+G models. * DT MODEL SELECTION : Best Model's command line phyml -i /tmp/jmodeltest4579695484136556156.phy -d nt -n 1 -b 0 --run_id F81+G -m 000000 -f m -c 4 -a e --no_memory_check -u /tmp/jmodeltest7971412443020107151.tree -o lr --------------------------------------------------------------- * * * MODEL AVERAGED PHYLOGENY * * * --------------------------------------------------------------- Selection criterion: . . . . DT Confidence interval: . . . . 1.00 Consensus type:. . . . . . . 50% majority rule Using 88 models in the 1.00 confidence interval = F81+G TPM1uf+G HKY+G TPM3uf+G TVM+G TPM2uf+G TrN+G TIM2+G TIM1+G GTR+G K80+G TPM3+G TPM1+G TIM3+G JC+G TPM2+G TVMef+G TrNef+G TIM3ef+G TIM1ef+G TIM2ef+G SYM+G TIM2ef+I+G SYM+I+G GTR+I+G TrNef+I+G TIM3+I+G TIM1ef+I+G TIM3ef+I+G TIM2+I+G TIM1+I+G TVM+I+G TrN+I+G TPM2+I+G TVMef+I+G TPM3uf+I+G TPM2uf+I+G TPM1uf+I+G F81+I+G HKY+I+G JC+I+G TPM1+I+G K80+I+G TPM3+I+G JC F81 K80 HKY TrNef TrN TPM1 TPM1uf TPM2 TPM2uf TPM3 TPM3uf TIM1ef TIM1 TIM2ef TIM2 TIM3ef TIM3 TVMef TVM SYM GTR TIM2ef+I SYM+I TrNef+I TIM1ef+I TIM3ef+I TPM2+I TVMef+I TPM3uf+I TPM1uf+I HKY+I F81+I TVM+I TIM3+I GTR+I TIM1+I TrN+I TPM2uf+I TIM2+I TPM1+I K80+I JC+I TPM3+I Species in order: 1. P4 2. P6 3. P1 4. P5 5. P3 6. P2 Bipartitions included in the consensus tree 123456 ****** ( 1.0 ) ****-- ( 1.0 ) ***--- ( 1.0 ) -**--- ( 1.0 ) +-6 P1 +---7 | +-------------5 P6 +---8 | +---------------4 P4 +---------------------9 | +------------------3 P5 | +----------2 P2 | +------------------------------1 P3 (P3:0.014985,P2:0.005322,(P5:0.009268,(P4:0.007946,(P6:0.006687,P1:0.000000)1.00:0.002110)1.00:0.001994)1.00:0.010770); Note: this tree is unrooted. Branch lengths are the expected number of substitutions per site. Labels next to parentheses represent phylogenetic uncertainty due to model selection (see documentation) --------------------------------------------------------------- * * * HIERARCHICAL LIKELIHOO RATIO TESTS (hLRT) * * * --------------------------------------------------------------- Settings: Forward selection (adding parameters) starting model = JC hypotheses order = freq-titv-2ti-2tv-4tv-gamma-pinv Confidence alpha level = 0.0100 * Tested hypothesis = freq Null model = JC -lnL = 1115.6846 Alternative model = F81 -lnL = 1065.5537 2(lnL1-lnL0) = 100.2617 P-value < 1.0E-6 * Tested hypothesis = titv Null model = F81 -lnL = 1065.5537 Alternative model = HKY -lnL = 1065.0272 2(lnL1-lnL0) = 1.0529 P-value = 0.3048 The current model could not be rejected Model selected: Model = F81 partition = 000000 -lnL = 1065.5537 K = 12 freqA = 0.4207 freqC = 0.1546 freqG = 0.2019 freqT = 0.2229 -- PAUP* Commands Block: If you want to load the selected model and associated estimates in PAUP*, attach the next block of commands after the data in your PAUP file: [! Likelihood settings from best-fit model (F81) selected by hLRT with jModeltest 2.1.6 v20140903 on Wed Sep 17 07:31:19 PDT 2014] BEGIN PAUP; Lset base=(0.4207 0.1546 0.2019 ) nst=1 rates=equal pinvar=0; END; -- --------------------------------------------------------------- * * * SELECTION SUMMARY * * * --------------------------------------------------------------- ::Optimized Topologies Summary:: There are 1 different topologies. Topology Id: 1 Rank Weight RF AvgEucl VarEucl AIC 1 100.00% 0 2.62e-03 2.14e-06 BIC 1 100.00% 0 3.76e-03 5.86e-06 AICc 1 100.00% 0 2.62e-03 2.14e-06 DT 1 100.00% 0 3.76e-03 5.86e-06 Models supporting: 88 JC JC+I JC+G JC+I+G F81 F81+I F81+G F81+I+G K80 K80+I K80+G K80+I+G HKY HKY+I HKY+G HKY+I+G TrNef TrNef+I TrNef+G TrNef+I+G TrN TrN+I TrN+G TrN+I+G TPM1 TPM1+I TPM1+G TPM1+I+G TPM1uf TPM1uf+I TPM1uf+G TPM1uf+I+G TPM2 TPM2+I TPM2+G TPM2+I+G TPM2uf TPM2uf+I TPM2uf+G TPM2uf+I+G TPM3 TPM3+I TPM3+G TPM3+I+G TPM3uf TPM3uf+I TPM3uf+G TPM3uf+I+G TIM1ef TIM1ef+I TIM1ef+G TIM1ef+I+G TIM1 TIM1+I TIM1+G TIM1+I+G TIM2ef TIM2ef+I TIM2ef+G TIM2ef+I+G TIM2 TIM2+I TIM2+G TIM2+I+G TIM3ef TIM3ef+I TIM3ef+G TIM3ef+I+G TIM3 TIM3+I TIM3+G TIM3+I+G TVMef TVMef+I TVMef+G TVMef+I+G TVM TVM+I TVM+G TVM+I+G SYM SYM+I SYM+G SYM+I+G GTR GTR+I GTR+G GTR+I+G ::Best Models:: Model f(a) f(c) f(g) f(t) kappa titv Ra Rb Rc Rd Re Rf pInv gamma ---------------------------------------------------------------------------------------------------------------------------------------- AIC F81+I+G 0.42 0.15 0.20 0.22 0.00 0.00 1.000 1.000 1.000 1.000 1.000 1.000 0.27 0.01 BIC F81+G 0.42 0.15 0.20 0.22 0.00 0.00 1.000 1.000 1.000 1.000 1.000 1.000 N/A 0.02 AICc F81+I+G 0.42 0.15 0.20 0.22 0.00 0.00 1.000 1.000 1.000 1.000 1.000 1.000 0.27 0.01 DT F81+G 0.42 0.15 0.20 0.22 0.00 0.00 1.000 1.000 1.000 1.000 1.000 1.000 N/A 0.02 Program is done.