jmodeltest2_xsede this test runs. it can take a while, wall time is set long. command line we want: set by hidden params, requies the specified input file: (java -jar /opt/jmodeltest2/jModelTest.jar -tr 8 -d infile.phy) user configured: -s 11 excl 3 5 7 11 203 (default for set_subschemes_ = 11) -f switch 0 or 1 (default for uneq_basefmodels_ = 1) -i switch 0 or 1 (default for invar_models_ = 1_ -g 4 integer (default for numratecat_models_=4) -S NNI excl (default for def_topsearch_ = BEST) -AIC list, can choose multiple (no default for criteria_1_=-AICc,-BIC,-DT, -AIC) -p switch (default for parameter_importances_=1) -a swtich 0 or 1 (estimate_modelavg_ default =1) -w switch 1 or 0 (print_paup_ default = 1) Settings: toolId = JMODELTEST2_XSEDE runtime_=0.5 currently gives: 'java -jar /opt/jmodeltest2/jModelTest.jar -tr 8 -d infile.phy) -s 11 -f -i -g 4 -S NNI -AIC -p -a -w' STDOUT it produces: -------------------------- 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 Mar 04 12:52:12 PST 2015 Linux 2.6.32-431.29.2.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 -S NNI -AIC -p -a -w Reading data file "infile.phy"... OK. number of sequences: 92 number of sites: 5363 --------------------------------------------------------------- * * * 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 + 181 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:04:29:00 00h:04:29:01 23672.7001 (1/88) TPM3uf+I+G 00h:04:48:09 00h:04:48:09 23456.6638 (2/88) TPM2uf+I+G 00h:04:58:02 00h:04:58:02 23436.2045 (3/88) TPM1uf+I+G 00h:05:06:01 00h:05:06:01 23456.4873 (4/88) HKY+I+G 00h:10:33:04 00h:10:33:04 23461.0444 (5/88) TIM2+I+G 00h:10:59:03 00h:10:59:03 23429.8099 (6/88) TrN+I+G 00h:11:04:08 00h:11:04:08 23452.8288 (7/88) TIM1+I+G 00h:11:35:06 00h:11:35:06 23448.3188 (8/88) JC+I+G 00h:07:45:05 00h:12:51:05 23866.1888 (9/88) TVM+I+G 00h:09:10:06 00h:13:59:05 23429.4543 (10/88) TIM3+I+G 00h:10:17:00 00h:14:46:00 23447.0160 (11/88) GTR+I+G 00h:10:29:03 00h:15:27:05 23422.4583 (12/88) K80+I+G 00h:07:52:08 00h:18:26:01 23672.7708 (13/88) TPM2+I+G 00h:08:41:00 00h:20:16:06 23672.7299 (14/88) TPM1+I+G 00h:09:41:07 00h:20:46:05 23671.3357 (15/88) TPM3+I+G 00h:09:41:06 00h:22:33:02 23670.9253 (16/88) F81+G 00h:02:21:09 00h:23:08:04 23745.9966 (17/88) TrNef+I+G 00h:12:29:03 00h:23:28:06 23666.0940 (18/88) TIM1ef+I+G 00h:10:02:01 00h:24:01:06 23664.7134 (19/88) HKY+G 00h:02:01:08 00h:24:35:00 23533.9262 (20/88) TrN+G 00h:03:03:01 00h:26:11:05 23523.7400 (21/88) TVMef+I+G 00h:08:13:06 00h:26:39:08 23669.2203 (22/88) TPM1uf+G 00h:03:38:04 00h:27:07:00 23529.2967 (23/88) TPM2uf+G 00h:03:10:06 00h:27:12:02 23509.4298 (24/88) TPM3uf+G 00h:02:55:03 00h:27:30:03 23528.1961 (25/88) TIM1+G 00h:02:03:01 00h:28:14:06 23519.1008 (26/88) TIM2+G 00h:01:58:03 00h:28:38:01 23500.9367 (27/88) TVM+G 00h:01:50:03 00h:29:02:05 23502.0521 (28/88) TIM2ef+I+G 00h:14:17:08 00h:29:03:09 23666.0880 (29/88) TIM3ef+I+G 00h:13:52:09 00h:29:20:04 23664.1896 (30/88) GTR+G 00h:02:03:04 00h:29:33:07 23492.9823 (31/88) JC+G 00h:01:38:09 00h:29:53:05 23941.6111 (32/88) TIM3+G 00h:03:11:06 00h:30:18:07 23517.3831 (33/88) K80+G 00h:01:43:08 00h:30:21:09 23748.8895 (34/88) TPM1+G 00h:01:42:07 00h:30:46:06 23747.4859 (35/88) SYM+I+G 00h:10:40:05 00h:30:57:01 23662.5096 (36/88) TPM2+G 00h:02:00:09 00h:31:21:03 23748.7467 (37/88) TrNef+G 00h:02:25:02 00h:31:27:07 23740.5125 (38/88) TPM3+G 00h:02:47:06 00h:32:21:03 23747.4508 (39/88) TIM1ef+G 00h:02:49:00 00h:32:42:05 23739.3141 (40/88) HKY+I 00h:01:24:00 00h:32:51:07 23633.8547 (41/88) F81+I 00h:01:39:09 00h:33:01:02 23861.1745 (42/88) TIM3ef+G 00h:02:48:09 00h:33:10:08 23739.1377 (43/88) TVMef+G 00h:02:38:05 00h:33:25:01 23745.9170 (44/88) TIM2ef+G 00h:03:10:01 00h:33:28:08 23740.6415 (45/88) TPM1uf+I 00h:01:16:08 00h:33:59:03 23630.3011 (46/88) TPM2uf+I 00h:01:32:04 00h:34:24:02 23617.8864 (47/88) TrN+I 00h:02:06:00 00h:34:27:03 23624.3741 (48/88) SYM+G 00h:04:02:02 00h:34:59:03 23737.5143 (49/88) TIM1+I 00h:01:53:09 00h:35:04:07 23620.8130 (50/88) TPM3uf+I 00h:02:03:05 00h:35:04:07 23630.7678 (51/88) TIM2+I 00h:02:17:06 00h:35:42:06 23607.9316 (52/88) TIM3+I 00h:02:14:00 00h:35:42:08 23621.4148 (53/88) JC+I 00h:01:34:06 00h:36:01:09 24052.3393 (54/88) TVM+I 00h:02:18:00 00h:36:17:03 23613.1978 (55/88) GTR+I 00h:02:23:01 00h:36:47:03 23603.3788 (56/88) K80+I 00h:01:55:07 00h:36:55:00 23839.1405 (57/88) TPM1+I 00h:01:53:08 00h:36:58:05 23840.5104 (58/88) TrNef+I 00h:01:56:03 00h:37:01:00 23834.1493 (59/88) TPM3+I 00h:01:54:02 00h:37:36:09 23840.3324 (60/88) TPM2+I 00h:01:55:09 00h:37:38:05 23841.6857 (61/88) TIM1ef+I 00h:02:00:08 00h:38:02:08 23834.4764 (62/88) TIM2ef+I 00h:01:58:09 00h:38:16:02 23831.7086 (63/88) F81 00h:01:19:02 00h:38:20:02 24755.7597 (64/88) TIM3ef+I 00h:01:55:00 00h:38:42:03 23834.1681 (65/88) TVMef+I 00h:01:59:05 00h:38:54:05 23838.8028 (66/88) SYM+I 00h:02:06:02 00h:39:04:06 23831.1174 (67/88) HKY 00h:01:42:02 00h:39:19:01 24525.7694 (68/88) TrN 00h:01:42:00 00h:39:20:05 24500.6198 (69/88) TPM1uf 00h:01:39:01 00h:39:41:08 24513.9121 (70/88) TPM2uf 00h:01:43:03 00h:39:59:04 24493.1217 (71/88) TPM3uf 00h:01:48:05 00h:40:08:07 24512.2925 (72/88) TIM1 00h:01:44:02 00h:40:26:05 24498.5266 (73/88) TIM2 00h:01:48:06 00h:40:43:01 24473.9593 (74/88) TIM3 00h:01:48:06 00h:40:53:03 24491.6326 (75/88) JC 00h:01:15:09 00h:40:57:08 24978.9132 (76/88) TVM 00h:01:44:03 00h:41:03:05 24478.3480 (77/88) GTR 00h:01:53:09 00h:41:14:04 24458.7553 (78/88) K80 00h:01:27:08 00h:41:27:02 24780.9004 (79/88) TPM1 00h:01:11:05 00h:41:38:00 24774.5883 (80/88) TPM3 00h:00:57:05 00h:41:50:08 24777.8399 (81/88) TrNef 00h:01:43:09 00h:41:52:06 24756.3414 (82/88) TIM2ef 00h:00:53:08 00h:41:57:03 24751.9848 (83/88) TPM2 00h:01:26:04 00h:42:09:05 24773.8025 (84/88) TIM1ef 00h:01:30:07 00h:42:28:05 24758.1648 (85/88) TVMef 00h:01:04:08 00h:42:32:01 24772.6637 (86/88) TIM3ef 00h:01:22:02 00h:42:36:06 24758.8466 (87/88) SYM 00h:01:19:07 00h:42:57:07 24750.8493 (88/88) Model = JC partition = 000000 -lnL = 24978.9132 K = 182 Model = JC+I partition = 000000 -lnL = 24052.3393 K = 183 p-inv = 0.6680 Model = JC+G partition = 000000 -lnL = 23941.6111 K = 183 gamma shape = 0.2120 Model = JC+I+G partition = 000000 -lnL = 23866.1888 K = 184 p-inv = 0.5290 gamma shape = 0.7550 Model = F81 partition = 000000 -lnL = 24755.7597 K = 185 freqA = 0.3188 freqC = 0.1957 freqG = 0.1866 freqT = 0.2989 Model = F81+I partition = 000000 -lnL = 23861.1744 K = 186 freqA = 0.3136 freqC = 0.1990 freqG = 0.1876 freqT = 0.2998 p-inv = 0.6650 Model = F81+G partition = 000000 -lnL = 23745.9965 K = 186 freqA = 0.3125 freqC = 0.1999 freqG = 0.1879 freqT = 0.2997 gamma shape = 0.2170 Model = F81+I+G partition = 000000 -lnL = 23672.7001 K = 187 freqA = 0.3115 freqC = 0.2006 freqG = 0.1878 freqT = 0.3001 p-inv = 0.5250 gamma shape = 0.7610 Model = K80 partition = 010010 -lnL = 24780.9004 K = 183 kappa = 2.2291 (ti/tv = 1.1145) Model = K80+I partition = 010010 -lnL = 23839.1405 K = 184 kappa = 2.2827 (ti/tv = 1.1413) p-inv = 0.6900 Model = K80+G partition = 010010 -lnL = 23748.8895 K = 184 kappa = 2.2866 (ti/tv = 1.1433) gamma shape = 0.2110 Model = K80+I+G partition = 010010 -lnL = 23672.7708 K = 185 kappa = 2.2987 (ti/tv = 1.1493) p-inv = 0.5320 gamma shape = 0.7590 Model = HKY partition = 010010 -lnL = 24525.7694 K = 186 freqA = 0.3226 freqC = 0.1929 freqG = 0.1811 freqT = 0.3033 kappa = 2.3921 (ti/tv = 1.1191) Model = HKY+I partition = 010010 -lnL = 23633.8547 K = 187 freqA = 0.3167 freqC = 0.1972 freqG = 0.1866 freqT = 0.2995 kappa = 2.3672 (ti/tv = 1.1189) p-inv = 0.6830 Model = HKY+G partition = 010010 -lnL = 23533.9262 K = 187 freqA = 0.3187 freqC = 0.1960 freqG = 0.1849 freqT = 0.3004 kappa = 2.3918 (ti/tv = 1.1271) gamma shape = 0.2210 Model = HKY+I+G partition = 010010 -lnL = 23461.0444 K = 188 freqA = 0.3182 freqC = 0.1963 freqG = 0.1851 freqT = 0.3004 kappa = 2.3993 (ti/tv = 1.1312) p-inv = 0.5220 gamma shape = 0.7560 Model = TrNef partition = 010020 -lnL = 24756.3414 K = 184 R(a) [AC] = 1.0000 R(b) [AG] = 1.8547 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.6394 R(f) [GT] = 1.0000 Model = TrNef+I partition = 010020 -lnL = 23834.1493 K = 185 R(a) [AC] = 1.0000 R(b) [AG] = 2.0057 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.5621 R(f) [GT] = 1.0000 p-inv = 0.6890 Model = TrNef+G partition = 010020 -lnL = 23740.5125 K = 185 R(a) [AC] = 1.0000 R(b) [AG] = 1.9732 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.6009 R(f) [GT] = 1.0000 gamma shape = 0.2130 Model = TrNef+I+G partition = 010020 -lnL = 23666.0940 K = 186 R(a) [AC] = 1.0000 R(b) [AG] = 2.0017 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.5776 R(f) [GT] = 1.0000 p-inv = 0.5310 gamma shape = 0.7630 Model = TrN partition = 010020 -lnL = 24500.6198 K = 187 freqA = 0.3310 freqC = 0.1852 freqG = 0.1885 freqT = 0.2953 R(a) [AC] = 1.0000 R(b) [AG] = 1.9412 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.8900 R(f) [GT] = 1.0000 Model = TrN+I partition = 010020 -lnL = 23624.3741 K = 188 freqA = 0.3237 freqC = 0.1922 freqG = 0.1915 freqT = 0.2926 R(a) [AC] = 1.0000 R(b) [AG] = 2.0173 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.7269 R(f) [GT] = 1.0000 p-inv = 0.6810 Model = TrN+G partition = 010020 -lnL = 23523.7400 K = 188 freqA = 0.3261 freqC = 0.1901 freqG = 0.1908 freqT = 0.2931 R(a) [AC] = 1.0000 R(b) [AG] = 1.9905 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.8144 R(f) [GT] = 1.0000 gamma shape = 0.2230 Model = TrN+I+G partition = 010020 -lnL = 23452.8288 K = 189 freqA = 0.3259 freqC = 0.1912 freqG = 0.1898 freqT = 0.2930 R(a) [AC] = 1.0000 R(b) [AG] = 2.0359 R(c) [AT] = 1.0000 R(d) [CG] = 1.0000 R(e) [CT] = 2.7996 R(f) [GT] = 1.0000 p-inv = 0.5210 gamma shape = 0.7610 Model = TPM1 partition = 012210 -lnL = 24774.5883 K = 184 R(a) [AC] = 1.0000 R(b) [AG] = 2.1294 R(c) [AT] = 0.9083 R(d) [CG] = 0.9083 R(e) [CT] = 2.1294 R(f) [GT] = 1.0000 Model = TPM1+I partition = 012210 -lnL = 23840.5104 K = 185 R(a) [AC] = 1.0000 R(b) [AG] = 2.1818 R(c) [AT] = 0.9067 R(d) [CG] = 0.9067 R(e) [CT] = 2.1818 R(f) [GT] = 1.0000 p-inv = 0.6900 Model = TPM1+G partition = 012210 -lnL = 23747.4859 K = 185 R(a) [AC] = 1.0000 R(b) [AG] = 2.1793 R(c) [AT] = 0.9050 R(d) [CG] = 0.9050 R(e) [CT] = 2.1793 R(f) [GT] = 1.0000 gamma shape = 0.2110 Model = TPM1+I+G partition = 012210 -lnL = 23671.3357 K = 186 R(a) [AC] = 1.0000 R(b) [AG] = 2.1799 R(c) [AT] = 0.9006 R(d) [CG] = 0.9006 R(e) [CT] = 2.1799 R(f) [GT] = 1.0000 p-inv = 0.5320 gamma shape = 0.7580 Model = TPM1uf partition = 012210 -lnL = 24513.9121 K = 187 freqA = 0.3236 freqC = 0.1916 freqG = 0.1799 freqT = 0.3049 R(a) [AC] = 1.0000 R(b) [AG] = 2.1305 R(c) [AT] = 0.7925 R(d) [CG] = 0.7925 R(e) [CT] = 2.1305 R(f) [GT] = 1.0000 Model = TPM1uf+I partition = 012210 -lnL = 23630.3011 K = 188 freqA = 0.3172 freqC = 0.1966 freqG = 0.1862 freqT = 0.3001 R(a) [AC] = 1.0000 R(b) [AG] = 2.1798 R(c) [AT] = 0.8452 R(d) [CG] = 0.8452 R(e) [CT] = 2.1798 R(f) [GT] = 1.0000 p-inv = 0.6820 Model = TPM1uf+G partition = 012210 -lnL = 23529.2967 K = 188 freqA = 0.3195 freqC = 0.1950 freqG = 0.1842 freqT = 0.3014 R(a) [AC] = 1.0000 R(b) [AG] = 2.1766 R(c) [AT] = 0.8246 R(d) [CG] = 0.8246 R(e) [CT] = 2.1766 R(f) [GT] = 1.0000 gamma shape = 0.2220 Model = TPM1uf+I+G partition = 012210 -lnL = 23456.4873 K = 189 freqA = 0.3199 freqC = 0.1957 freqG = 0.1838 freqT = 0.3006 R(a) [AC] = 1.0000 R(b) [AG] = 2.1970 R(c) [AT] = 0.8262 R(d) [CG] = 0.8262 R(e) [CT] = 2.1970 R(f) [GT] = 1.0000 p-inv = 0.5210 gamma shape = 0.7540 Model = TPM2 partition = 010212 -lnL = 24773.8025 K = 184 R(a) [AC] = 0.8357 R(b) [AG] = 2.0200 R(c) [AT] = 0.8357 R(d) [CG] = 1.0000 R(e) [CT] = 2.0200 R(f) [GT] = 1.0000 Model = TPM2+I partition = 010212 -lnL = 23841.6857 K = 185 R(a) [AC] = 1.0210 R(b) [AG] = 2.3154 R(c) [AT] = 1.0210 R(d) [CG] = 1.0000 R(e) [CT] = 2.3154 R(f) [GT] = 1.0000 p-inv = 0.6900 Model = TPM2+G partition = 010212 -lnL = 23748.7467 K = 185 R(a) [AC] = 1.0097 R(b) [AG] = 2.3006 R(c) [AT] = 1.0097 R(d) [CG] = 1.0000 R(e) [CT] = 2.3006 R(f) [GT] = 1.0000 gamma shape = 0.2110 Model = TPM2+I+G partition = 010212 -lnL = 23672.7299 K = 186 R(a) [AC] = 1.0196 R(b) [AG] = 2.3226 R(c) [AT] = 1.0196 R(d) [CG] = 1.0000 R(e) [CT] = 2.3226 R(f) [GT] = 1.0000 p-inv = 0.5320 gamma shape = 0.7590 Model = TPM2uf partition = 010212 -lnL = 24493.1217 K = 187 freqA = 0.3316 freqC = 0.1925 freqG = 0.1728 freqT = 0.3030 R(a) [AC] = 0.6025 R(b) [AG] = 1.7807 R(c) [AT] = 0.6025 R(d) [CG] = 1.0000 R(e) [CT] = 1.7807 R(f) [GT] = 1.0000 Model = TPM2uf+I partition = 010212 -lnL = 23617.8864 K = 188 freqA = 0.3256 freqC = 0.1965 freqG = 0.1790 freqT = 0.2989 R(a) [AC] = 0.6795 R(b) [AG] = 1.9082 R(c) [AT] = 0.6795 R(d) [CG] = 1.0000 R(e) [CT] = 1.9082 R(f) [GT] = 1.0000 p-inv = 0.6790 Model = TPM2uf+G partition = 010212 -lnL = 23509.4298 K = 188 freqA = 0.3318 freqC = 0.1951 freqG = 0.1736 freqT = 0.2995 R(a) [AC] = 0.6021 R(b) [AG] = 1.8042 R(c) [AT] = 0.6021 R(d) [CG] = 1.0000 R(e) [CT] = 1.8042 R(f) [GT] = 1.0000 gamma shape = 0.2260 Model = TPM2uf+I+G partition = 010212 -lnL = 23436.2045 K = 189 freqA = 0.3329 freqC = 0.1957 freqG = 0.1727 freqT = 0.2986 R(a) [AC] = 0.5959 R(b) [AG] = 1.8106 R(c) [AT] = 0.5959 R(d) [CG] = 1.0000 R(e) [CT] = 1.8106 R(f) [GT] = 1.0000 p-inv = 0.5150 gamma shape = 0.7410 Model = TPM3 partition = 012012 -lnL = 24777.8399 K = 184 R(a) [AC] = 1.0596 R(b) [AG] = 2.2904 R(c) [AT] = 1.0000 R(d) [CG] = 1.0596 R(e) [CT] = 2.2904 R(f) [GT] = 1.0000 Model = TPM3+I partition = 012012 -lnL = 23840.3324 K = 185 R(a) [AC] = 0.8991 R(b) [AG] = 2.1787 R(c) [AT] = 1.0000 R(d) [CG] = 0.8991 R(e) [CT] = 2.1787 R(f) [GT] = 1.0000 p-inv = 0.6910 Model = TPM3+G partition = 012012 -lnL = 23747.4508 K = 185 R(a) [AC] = 0.8993 R(b) [AG] = 2.1775 R(c) [AT] = 1.0000 R(d) [CG] = 0.8993 R(e) [CT] = 2.1775 R(f) [GT] = 1.0000 gamma shape = 0.2100 Model = TPM3+I+G partition = 012012 -lnL = 23670.9253 K = 186 R(a) [AC] = 0.8817 R(b) [AG] = 2.1633 R(c) [AT] = 1.0000 R(d) [CG] = 0.8817 R(e) [CT] = 2.1633 R(f) [GT] = 1.0000 p-inv = 0.5330 gamma shape = 0.7570 Model = TPM3uf partition = 012012 -lnL = 24512.2925 K = 187 freqA = 0.3224 freqC = 0.1872 freqG = 0.1809 freqT = 0.3094 R(a) [AC] = 1.3855 R(b) [AG] = 2.7528 R(c) [AT] = 1.0000 R(d) [CG] = 1.3855 R(e) [CT] = 2.7528 R(f) [GT] = 1.0000 Model = TPM3uf+I partition = 012012 -lnL = 23630.7678 K = 188 freqA = 0.3165 freqC = 0.1941 freqG = 0.1864 freqT = 0.3030 R(a) [AC] = 1.1822 R(b) [AG] = 2.5534 R(c) [AT] = 1.0000 R(d) [CG] = 1.1822 R(e) [CT] = 2.5534 R(f) [GT] = 1.0000 p-inv = 0.6820 Model = TPM3uf+G partition = 012012 -lnL = 23528.1961 K = 188 freqA = 0.3184 freqC = 0.1909 freqG = 0.1846 freqT = 0.3061 R(a) [AC] = 1.2717 R(b) [AG] = 2.6672 R(c) [AT] = 1.0000 R(d) [CG] = 1.2717 R(e) [CT] = 2.6672 R(f) [GT] = 1.0000 gamma shape = 0.2230 Model = TPM3uf+I+G partition = 012012 -lnL = 23456.6638 K = 189 freqA = 0.3180 freqC = 0.1910 freqG = 0.1849 freqT = 0.3062 R(a) [AC] = 1.2722 R(b) [AG] = 2.6873 R(c) [AT] = 1.0000 R(d) [CG] = 1.2722 R(e) [CT] = 2.6873 R(f) [GT] = 1.0000 p-inv = 0.5210 gamma shape = 0.7560 Model = TIM1ef partition = 012230 -lnL = 24758.1648 K = 185 R(a) [AC] = 1.0000 R(b) [AG] = 1.7768 R(c) [AT] = 0.9126 R(d) [CG] = 0.9126 R(e) [CT] = 2.5155 R(f) [GT] = 1.0000 Model = TIM1ef+I partition = 012230 -lnL = 23834.4764 K = 186 R(a) [AC] = 1.0000 R(b) [AG] = 1.9073 R(c) [AT] = 0.9046 R(d) [CG] = 0.9046 R(e) [CT] = 2.4364 R(f) [GT] = 1.0000 p-inv = 0.6890 Model = TIM1ef+G partition = 012230 -lnL = 23739.3141 K = 186 R(a) [AC] = 1.0000 R(b) [AG] = 1.8749 R(c) [AT] = 0.9031 R(d) [CG] = 0.9031 R(e) [CT] = 2.4712 R(f) [GT] = 1.0000 gamma shape = 0.2130 Model = TIM1ef+I+G partition = 012230 -lnL = 23664.7134 K = 187 R(a) [AC] = 1.0000 R(b) [AG] = 1.9013 R(c) [AT] = 0.9007 R(d) [CG] = 0.9007 R(e) [CT] = 2.4483 R(f) [GT] = 1.0000 p-inv = 0.5300 gamma shape = 0.7630 Model = TIM1 partition = 012230 -lnL = 24498.5266 K = 188 freqA = 0.3316 freqC = 0.1843 freqG = 0.1879 freqT = 0.2962 R(a) [AC] = 1.0000 R(b) [AG] = 1.7351 R(c) [AT] = 0.7968 R(d) [CG] = 0.7968 R(e) [CT] = 2.5708 R(f) [GT] = 1.0000 Model = TIM1+I partition = 012230 -lnL = 23620.8129 K = 189 freqA = 0.3241 freqC = 0.1916 freqG = 0.1910 freqT = 0.2933 R(a) [AC] = 1.0000 R(b) [AG] = 1.8571 R(c) [AT] = 0.8454 R(d) [CG] = 0.8454 R(e) [CT] = 2.5110 R(f) [GT] = 1.0000 p-inv = 0.6800 Model = TIM1+G partition = 012230 -lnL = 23519.1008 K = 189 freqA = 0.3268 freqC = 0.1891 freqG = 0.1901 freqT = 0.2941 R(a) [AC] = 1.0000 R(b) [AG] = 1.8101 R(c) [AT] = 0.8246 R(d) [CG] = 0.8246 R(e) [CT] = 2.5625 R(f) [GT] = 1.0000 gamma shape = 0.2240 Model = TIM1+I+G partition = 012230 -lnL = 23448.3188 K = 190 freqA = 0.3266 freqC = 0.1903 freqG = 0.1891 freqT = 0.2940 R(a) [AC] = 1.0000 R(b) [AG] = 1.8538 R(c) [AT] = 0.8255 R(d) [CG] = 0.8255 R(e) [CT] = 2.5497 R(f) [GT] = 1.0000 p-inv = 0.5200 gamma shape = 0.7610 Model = TIM2ef partition = 010232 -lnL = 24751.9848 K = 185 R(a) [AC] = 0.8383 R(b) [AG] = 1.6818 R(c) [AT] = 0.8383 R(d) [CG] = 1.0000 R(e) [CT] = 2.3923 R(f) [GT] = 1.0000 Model = TIM2ef+I partition = 010232 -lnL = 23831.7086 K = 186 R(a) [AC] = 1.0102 R(b) [AG] = 2.0135 R(c) [AT] = 1.0102 R(d) [CG] = 1.0000 R(e) [CT] = 2.5640 R(f) [GT] = 1.0000 p-inv = 0.6890 Model = TIM2ef+G partition = 010232 -lnL = 23740.6415 K = 186 R(a) [AC] = 0.9949 R(b) [AG] = 1.9657 R(c) [AT] = 0.9949 R(d) [CG] = 1.0000 R(e) [CT] = 2.5914 R(f) [GT] = 1.0000 gamma shape = 0.2130 Model = TIM2ef+I+G partition = 010232 -lnL = 23666.0880 K = 187 R(a) [AC] = 1.0072 R(b) [AG] = 2.0092 R(c) [AT] = 1.0072 R(d) [CG] = 1.0000 R(e) [CT] = 2.5877 R(f) [GT] = 1.0000 p-inv = 0.5300 gamma shape = 0.7630 Model = TIM2 partition = 010232 -lnL = 24473.9593 K = 188 freqA = 0.3400 freqC = 0.1852 freqG = 0.1798 freqT = 0.2950 R(a) [AC] = 0.6070 R(b) [AG] = 1.4622 R(c) [AT] = 0.6070 R(d) [CG] = 1.0000 R(e) [CT] = 2.1452 R(f) [GT] = 1.0000 Model = TIM2+I partition = 010232 -lnL = 23607.9316 K = 189 freqA = 0.3330 freqC = 0.1915 freqG = 0.1837 freqT = 0.2919 R(a) [AC] = 0.6764 R(b) [AG] = 1.6168 R(c) [AT] = 0.6764 R(d) [CG] = 1.0000 R(e) [CT] = 2.1993 R(f) [GT] = 1.0000 p-inv = 0.6770 Model = TIM2+G partition = 010232 -lnL = 23500.9367 K = 189 freqA = 0.3378 freqC = 0.1897 freqG = 0.1796 freqT = 0.2929 R(a) [AC] = 0.6163 R(b) [AG] = 1.5430 R(c) [AT] = 0.6163 R(d) [CG] = 1.0000 R(e) [CT] = 2.1219 R(f) [GT] = 1.0000 gamma shape = 0.2280 Model = TIM2+I+G partition = 010232 -lnL = 23429.8099 K = 190 freqA = 0.3382 freqC = 0.1909 freqG = 0.1781 freqT = 0.2928 R(a) [AC] = 0.6092 R(b) [AG] = 1.5750 R(c) [AT] = 0.6092 R(d) [CG] = 1.0000 R(e) [CT] = 2.0936 R(f) [GT] = 1.0000 p-inv = 0.5140 gamma shape = 0.7480 Model = TIM3ef partition = 012032 -lnL = 24758.8466 K = 185 R(a) [AC] = 1.0600 R(b) [AG] = 1.9085 R(c) [AT] = 1.0000 R(d) [CG] = 1.0600 R(e) [CT] = 2.7022 R(f) [GT] = 1.0000 Model = TIM3ef+I partition = 012032 -lnL = 23834.1681 K = 186 R(a) [AC] = 0.8928 R(b) [AG] = 1.8976 R(c) [AT] = 1.0000 R(d) [CG] = 0.8928 R(e) [CT] = 2.4297 R(f) [GT] = 1.0000 p-inv = 0.6890 Model = TIM3ef+G partition = 012032 -lnL = 23739.1377 K = 186 R(a) [AC] = 0.8922 R(b) [AG] = 1.8658 R(c) [AT] = 1.0000 R(d) [CG] = 0.8922 R(e) [CT] = 2.4662 R(f) [GT] = 1.0000 gamma shape = 0.2120 Model = TIM3ef+I+G partition = 012032 -lnL = 23664.1896 K = 187 R(a) [AC] = 0.8783 R(b) [AG] = 1.8812 R(c) [AT] = 1.0000 R(d) [CG] = 0.8783 R(e) [CT] = 2.4280 R(f) [GT] = 1.0000 p-inv = 0.5310 gamma shape = 0.7610 Model = TIM3 partition = 012032 -lnL = 24491.6325 K = 188 freqA = 0.3307 freqC = 0.1799 freqG = 0.1887 freqT = 0.3008 R(a) [AC] = 1.3923 R(b) [AG] = 2.2368 R(c) [AT] = 1.0000 R(d) [CG] = 1.3923 R(e) [CT] = 3.3307 R(f) [GT] = 1.0000 Model = TIM3+I partition = 012032 -lnL = 23621.4148 K = 189 freqA = 0.3234 freqC = 0.1893 freqG = 0.1912 freqT = 0.2960 R(a) [AC] = 1.1775 R(b) [AG] = 2.1730 R(c) [AT] = 1.0000 R(d) [CG] = 1.1775 R(e) [CT] = 2.9331 R(f) [GT] = 1.0000 p-inv = 0.6800 Model = TIM3+G partition = 012032 -lnL = 23517.3831 K = 189 freqA = 0.3260 freqC = 0.1845 freqG = 0.1906 freqT = 0.2990 R(a) [AC] = 1.2924 R(b) [AG] = 2.2224 R(c) [AT] = 1.0000 R(d) [CG] = 1.2924 R(e) [CT] = 3.1793 R(f) [GT] = 1.0000 gamma shape = 0.2260 Model = TIM3+I+G partition = 012032 -lnL = 23447.0160 K = 190 freqA = 0.3258 freqC = 0.1857 freqG = 0.1897 freqT = 0.2989 R(a) [AC] = 1.2829 R(b) [AG] = 2.2647 R(c) [AT] = 1.0000 R(d) [CG] = 1.2829 R(e) [CT] = 3.1548 R(f) [GT] = 1.0000 p-inv = 0.5180 gamma shape = 0.7580 Model = TVMef partition = 012314 -lnL = 24772.6637 K = 186 R(a) [AC] = 0.8871 R(b) [AG] = 2.0078 R(c) [AT] = 0.7840 R(d) [CG] = 0.9862 R(e) [CT] = 2.0078 R(f) [GT] = 1.0000 Model = TVMef+I partition = 012314 -lnL = 23838.8028 K = 187 R(a) [AC] = 0.9192 R(b) [AG] = 2.0913 R(c) [AT] = 0.9254 R(d) [CG] = 0.7999 R(e) [CT] = 2.0913 R(f) [GT] = 1.0000 p-inv = 0.6910 Model = TVMef+G partition = 012314 -lnL = 23745.9170 K = 187 R(a) [AC] = 0.9085 R(b) [AG] = 2.0760 R(c) [AT] = 0.9146 R(d) [CG] = 0.7980 R(e) [CT] = 2.0760 R(f) [GT] = 1.0000 gamma shape = 0.2100 Model = TVMef+I+G partition = 012314 -lnL = 23669.2202 K = 188 R(a) [AC] = 0.8974 R(b) [AG] = 2.0636 R(c) [AT] = 0.9150 R(d) [CG] = 0.7774 R(e) [CT] = 2.0636 R(f) [GT] = 1.0000 p-inv = 0.5330 gamma shape = 0.7560 Model = TVM partition = 012314 -lnL = 24478.3480 K = 189 freqA = 0.3314 freqC = 0.1869 freqG = 0.1727 freqT = 0.3091 R(a) [AC] = 0.8346 R(b) [AG] = 1.9485 R(c) [AT] = 0.5486 R(d) [CG] = 1.2385 R(e) [CT] = 1.9485 R(f) [GT] = 1.0000 Model = TVM+I partition = 012314 -lnL = 23613.1978 K = 190 freqA = 0.3254 freqC = 0.1934 freqG = 0.1787 freqT = 0.3025 R(a) [AC] = 0.8064 R(b) [AG] = 1.9566 R(c) [AT] = 0.6153 R(d) [CG] = 1.0604 R(e) [CT] = 1.9566 R(f) [GT] = 1.0000 p-inv = 0.6770 Model = TVM+G partition = 012314 -lnL = 23502.0521 K = 190 freqA = 0.3314 freqC = 0.1900 freqG = 0.1733 freqT = 0.3053 R(a) [AC] = 0.7680 R(b) [AG] = 1.9077 R(c) [AT] = 0.5433 R(d) [CG] = 1.1309 R(e) [CT] = 1.9077 R(f) [GT] = 1.0000 gamma shape = 0.2290 Model = TVM+I+G partition = 012314 -lnL = 23429.4543 K = 191 freqA = 0.3325 freqC = 0.1908 freqG = 0.1724 freqT = 0.3043 R(a) [AC] = 0.7529 R(b) [AG] = 1.9060 R(c) [AT] = 0.5367 R(d) [CG] = 1.1190 R(e) [CT] = 1.9060 R(f) [GT] = 1.0000 p-inv = 0.5120 gamma shape = 0.7370 Model = SYM partition = 012345 -lnL = 24750.8492 K = 187 R(a) [AC] = 0.8840 R(b) [AG] = 1.6622 R(c) [AT] = 0.7829 R(d) [CG] = 0.9732 R(e) [CT] = 2.3630 R(f) [GT] = 1.0000 Model = SYM+I partition = 012345 -lnL = 23831.1174 K = 188 R(a) [AC] = 0.9063 R(b) [AG] = 1.8165 R(c) [AT] = 0.9172 R(d) [CG] = 0.7960 R(e) [CT] = 2.3251 R(f) [GT] = 1.0000 p-inv = 0.6890 Model = SYM+G partition = 012345 -lnL = 23737.5143 K = 188 R(a) [AC] = 0.8927 R(b) [AG] = 1.7706 R(c) [AT] = 0.9044 R(d) [CG] = 0.7926 R(e) [CT] = 2.3413 R(f) [GT] = 1.0000 gamma shape = 0.2120 Model = SYM+I+G partition = 012345 -lnL = 23662.5096 K = 189 R(a) [AC] = 0.8859 R(b) [AG] = 1.7868 R(c) [AT] = 0.9068 R(d) [CG] = 0.7744 R(e) [CT] = 2.3047 R(f) [GT] = 1.0000 p-inv = 0.5310 gamma shape = 0.7620 Model = GTR partition = 012345 -lnL = 24458.7553 K = 190 freqA = 0.3399 freqC = 0.1798 freqG = 0.1797 freqT = 0.3007 R(a) [AC] = 0.8450 R(b) [AG] = 1.6003 R(c) [AT] = 0.5528 R(d) [CG] = 1.2450 R(e) [CT] = 2.3573 R(f) [GT] = 1.0000 Model = GTR+I partition = 012345 -lnL = 23603.3788 K = 191 freqA = 0.3327 freqC = 0.1885 freqG = 0.1834 freqT = 0.2954 R(a) [AC] = 0.8001 R(b) [AG] = 1.6582 R(c) [AT] = 0.6130 R(d) [CG] = 1.0569 R(e) [CT] = 2.2534 R(f) [GT] = 1.0000 p-inv = 0.6750 Model = GTR+G partition = 012345 -lnL = 23492.9823 K = 191 freqA = 0.3376 freqC = 0.1841 freqG = 0.1795 freqT = 0.2988 R(a) [AC] = 0.7981 R(b) [AG] = 1.6339 R(c) [AT] = 0.5569 R(d) [CG] = 1.1485 R(e) [CT] = 2.2739 R(f) [GT] = 1.0000 gamma shape = 0.2310 Model = GTR+I+G partition = 012345 -lnL = 23422.4583 K = 192 freqA = 0.3380 freqC = 0.1854 freqG = 0.1780 freqT = 0.2986 R(a) [AC] = 0.7825 R(b) [AG] = 1.6593 R(c) [AT] = 0.5496 R(d) [CG] = 1.1367 R(e) [CT] = 2.2356 R(f) [GT] = 1.0000 p-inv = 0.5110 gamma shape = 0.7440 Best-fit models should be reoptimized for comparison with unconstrained likelihood Computation of likelihood scores completed. It took 00h:42:57:07. --------------------------------------------------------------- * * * AKAIKE INFORMATION CRITERION (AIC) * * * --------------------------------------------------------------- Model selected: Model = GTR+I+G partition = 012345 -lnL = 23422.4583 K = 192 freqA = 0.3380 freqC = 0.1854 freqG = 0.1780 freqT = 0.2986 R(a) [AC] = 0.7825 R(b) [AG] = 1.6593 R(c) [AT] = 0.5496 R(d) [CG] = 1.1367 R(e) [CT] = 2.2356 R(f) [GT] = 1.0000 p-inv = 0.5110 gamma shape = 0.7440 -- 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 (GTR+I+G) selected by AIC with jModeltest 2.1.6 v20140903 on Wed Mar 04 13:35:11 PST 2015] BEGIN PAUP; Lset base=(0.3380 0.1854 0.1780 ) nst=6 rmat=(0.7825 1.6593 0.5496 1.1367 2.2356) rates=gamma shape=0.7440 ncat=4 pinvar=0.5110; END; -- Tree for the best AIC model = (Circaea_alpina_GB:0.00778037,Circaea_lutetiana_GB:0.00204496,((Fuchsia_cylindracea_F2:0.01545843,(Fuchsia_glazioviana_F3_nocontig:0.00716657,Fuchsia_lycioides_F4:0.00532756):0.00470527):0.00610583,(Hauya_heydeana_GB:0.02123338,(((L_ovalis_L3_4X:0.00593914,((L_linearis_L16_2X:0.00347243,L_linifolia_L9_2X:0.00421795):0.00469461,(((L_curtisii_L27_8X:0.00231411,(L_alata_L19_6X:0.00191656,((L_repens_L25_6X:0.00000003,L_repens_L42_6X:0.00000000):0.00123560,(L_arcuata_L38_4X:0.00125913,L_brevipes_L40_6X:0.00000002):0.00243515):0.00174512):0.00138352):0.00068186,(L_spathulata_L39_4X:0.00209576,(L_microcarpa_L13_2X:0.00023601,L_microcarpa_L22_2X:0.00049161):0.00364628):0.00000001):0.00046708,((L_polycarpa_L37_4X:0.00288235,(L_palustris_L26_2X:0.00098606,L_palustris_L41_2X:0.00063141):0.00049150):0.00149009,(L_sphaerocarpa_L18_4X:0.00363170,(L_glandulosa_L21_4X:0.00127123,(L_suffruticosa_L20_4X:0.00483291,(L_ravenii_L34_4X:0.00231777,(L_lanceolata_L17_4X:0.01138842,L_pilosa_L28_4X:0.00179851):0.00000004):0.00125600):0.00071202):0.00023505):0.00076168):0.00100575):0.00101120):0.00075125):0.00397782,((L_alternifolia_L10_2X:0.00193579,L_hirtella_L12_2X:0.00252543):0.00239733,(L_maritima_L15_2X:0.00816728,L_virgata_L11_2X:0.00487023):0.00206033):0.00543727):0.00998190,((L_torulosa_L132:0.01368509,((L_hexapetala_L2_10X:0.00000000,(L_grandiflora_L104_6XP:0.00022650,L_grandiflora_L108_6XP:0.00091667):0.00052120):0.00143058,((L_peploides_L79_2X:0.00259908,L_peploides_L8_2X:0.00229804):0.00130432,(L_stolonifera_L66_4X:0.00380815,(L_x_taiwanensis_L96_3X:0.00072559,(L_x_taiwanensis_L36_3X:0.00071316,L_adscendens_L93_4X:0.00191585):0.00069472):0.00351877):0.00147415):0.00041985):0.00822356):0.00340416,((((L_abyssinica_L65_6X:0.00748617,(L_stenorraphe_L51_12X:0.00220479,L_stenorraphe_L52_12X:0.00295198):0.00489732):0.00268371,(L_jussiaeoides_L33_M_8X:0.01199318,(L_hyssopifolia_L71_2X:0.00275801,(L_hyssopifolia_L32_M_2X:0.00286437,L_hyssopifolia_L73_2X:0.00000000):0.00016069):0.00490585):0.00305778):0.00224145,(L_quadrangularis_L129:0.00973940,(L_peruviana_L23_4X5X6X8X:0.01041140,(((L_leptocarpa_L102_4X6X:0.00272992,L_leptocarpa_L97_4X6X:0.00229983):0.00150919,(L_leptocarpa_L76_4X6X:0.00059246,(L_leptocarpa_L43_4X6X:0.00000000,L_leptocarpa_L49_4X6X:0.00063134):0.00094564):0.00133952):0.00541855,(L_rigida_L133_:0.00296058,(L_pseudonarcissus_L111_4X:0.00071482,L_pseudonarcissus_L128_4X:0.00138052):0.00040448):0.00079131):0.00290032):0.00134831):0.00081202):0.00446276,((L_perennis_L116_2X:0.00047719,L_perennis_L68_2X:0.00218339):0.01610787,(((L_martii_L113_6X:0.00838006,(((L_irwinii_L114_6X:0.01334607,L_myrtifolia_L115_6X:0.00371080):0.00440332,((L_sericea_L100_4X:0.00153746,L_sericea_L101_4X:0.00233878):0.00064628,(L_sericea_L112_4X:0.00470275,L_hassleriana_L107_4X:0.00834353):0.00123912):0.00120383):0.00164395,(L_elegans_L109_8X:0.00353335,(L_elegans_L103_8X:0.00189881,L_peruviana_L77_4X5X6X8X:0.00598984):0.01371342):0.00162104):0.00077999):0.00158872,((L_decurrens_L98_2X:0.00026391,(L_decurrens_L24_2X:0.00000000,L_decurrens_L82_2X:0.00000001):0.00028451):0.00727433,(L_sedoides_L7_2X:0.01430389,(L_inclinata_L120_2X:0.04062915,L_major_L99_2X:0.00673245):0.00228974):0.00107063):0.00026041):0.00144121,(((L_erecta_L44_2X:0.00074822,L_erecta_L95_2X:0.00074811):0.00677920,(L_nervosa_L106_2X:0.00000001,L_nervosa_L110:0.00049422):0.00432110):0.00512247,((L_bonariensis_L35_2X:0.00329089,((L_octovalvis_L54_2X:0.00360077,L_octovalvis_L55_2X:0.00057179):0.00155456,((L_neograndiflora_L105:0.00443032,L_neograndiflora_L59:0.00557588):0.00118379,(L_lagunae_L58_2X:0.00281607,(L_bonariensis_L56_2X:0.00034385,L_lagunae_L61_2X:0.00172205):0.00257754):0.00075253):0.00062379):0.00160515):0.00058071,(L_octovalvis_L53_4X:0.00195233,(L_octovalvis_L50_4X:0.00274310,(L_octovalvis_L69_6X:0.00131000,L_octovalvis_L62_4X:0.00000001):0.00000002):0.00095850):0.00068257):0.00417683):0.00034071):0.00432063):0.00061956):0.00179427):0.00499342):0.07733510):0.02312602):0.01694270); * AIC MODEL SELECTION : Selection uncertainty Model -lnL K AIC delta weight cumWeight ------------------------------------------------------------------------- GTR+I+G 23422.45827 192 47228.916540 0.000000 0.992801 0.992801 TIM2+I+G 23429.80985 190 47239.619700 10.703160 0.004707 0.997508 TVM+I+G 23429.45428 191 47240.908560 11.992020 0.002471 0.999979 TPM2uf+I+G 23436.20453 189 47250.409060 21.492520 2.14e-005 1.000000 TIM3+I+G 23447.01595 190 47274.031900 45.115360 1.59e-010 1.000000 TIM1+I+G 23448.31878 190 47276.637560 47.721020 4.31e-011 1.000000 TrN+I+G 23452.82877 189 47283.657540 54.741000 1.29e-012 1.000000 TPM1uf+I+G 23456.48728 189 47290.974560 62.058020 3.32e-014 1.000000 TPM3uf+I+G 23456.66377 189 47291.327540 62.411000 2.78e-014 1.000000 HKY+I+G 23461.04441 188 47298.088820 69.172280 9.47e-016 1.000000 GTR+G 23492.98226 191 47367.964520 139.047980 6.35e-031 1.000000 TIM2+G 23500.93674 189 47379.873480 150.956940 1.65e-033 1.000000 TVM+G 23502.05212 190 47384.104240 155.187700 1.99e-034 1.000000 TPM2uf+G 23509.42982 188 47394.859640 165.943100 9.18e-037 1.000000 TIM3+G 23517.38306 189 47412.766120 183.849580 1.19e-040 1.000000 TIM1+G 23519.10076 189 47416.201520 187.284980 2.13e-041 1.000000 TrN+G 23523.73998 188 47423.479960 194.563420 5.60e-043 1.000000 TPM3uf+G 23528.19608 188 47432.392160 203.475620 6.50e-045 1.000000 TPM1uf+G 23529.29668 188 47434.593360 205.676820 2.16e-045 1.000000 HKY+G 23533.92619 187 47441.852380 212.935840 5.73e-047 1.000000 GTR+I 23603.37877 191 47588.757540 359.841000 7.22e-079 1.000000 TIM2+I 23607.93162 189 47593.863240 364.946700 5.62e-080 1.000000 TVM+I 23613.19778 190 47606.395560 377.479020 1.07e-082 1.000000 TPM2uf+I 23617.88639 188 47611.772780 382.856240 7.26e-084 1.000000 TIM1+I 23620.81295 189 47619.625900 390.709360 1.43e-085 1.000000 TIM3+I 23621.41479 189 47620.829580 391.913040 7.83e-086 1.000000 TrN+I 23624.37411 188 47624.748220 395.831680 1.10e-086 1.000000 TPM1uf+I 23630.30112 188 47636.602240 407.685700 2.94e-089 1.000000 TPM3uf+I 23630.76777 188 47637.535540 408.619000 1.85e-089 1.000000 HKY+I 23633.85472 187 47641.709440 412.792900 2.29e-090 1.000000 TIM3ef+I+G 23664.18956 187 47702.379120 473.462580 1.53e-103 1.000000 SYM+I+G 23662.50961 189 47703.019220 474.102680 1.11e-103 1.000000 TIM1ef+I+G 23664.71343 187 47703.426860 474.510320 9.08e-104 1.000000 TrNef+I+G 23666.09400 186 47704.188000 475.271460 6.21e-104 1.000000 TIM2ef+I+G 23666.08797 187 47706.175940 477.259400 2.30e-104 1.000000 TPM3+I+G 23670.92534 186 47713.850680 484.934140 4.95e-106 1.000000 TVMef+I+G 23669.22025 188 47714.440500 485.523960 3.69e-106 1.000000 TPM1+I+G 23671.33567 186 47714.671340 485.754800 3.29e-106 1.000000 K80+I+G 23672.77081 185 47715.541620 486.625080 2.13e-106 1.000000 TPM2+I+G 23672.72986 186 47717.459720 488.543180 8.15e-107 1.000000 F81+I+G 23672.70008 187 47719.400160 490.483620 3.09e-107 1.000000 TIM3ef+G 23739.13773 186 47850.275460 621.358920 1.18e-135 1.000000 TIM1ef+G 23739.31413 186 47850.628260 621.711720 9.86e-136 1.000000 TrNef+G 23740.51249 185 47851.024980 622.108440 8.09e-136 1.000000 SYM+G 23737.51431 188 47851.028620 622.112080 8.07e-136 1.000000 TIM2ef+G 23740.64148 186 47853.282960 624.366420 2.61e-136 1.000000 F81+G 23745.99655 186 47863.993100 635.076560 1.24e-138 1.000000 TPM3+G 23747.45084 185 47864.901680 635.985140 7.84e-139 1.000000 TPM1+G 23747.48585 185 47864.971700 636.055160 7.57e-139 1.000000 K80+G 23748.88949 184 47865.778980 636.862440 5.06e-139 1.000000 TVMef+G 23745.91699 187 47865.833980 636.917440 4.92e-139 1.000000 TPM2+G 23748.74666 185 47867.493320 638.576780 2.15e-139 1.000000 TIM2ef+I 23831.70860 186 48035.417200 806.500660 7.37e-176 1.000000 SYM+I 23831.11737 188 48038.234740 809.318200 1.80e-176 1.000000 TrNef+I 23834.14931 185 48038.298620 809.382080 1.74e-176 1.000000 TIM3ef+I 23834.16805 186 48040.336100 811.419560 6.30e-177 1.000000 TIM1ef+I 23834.47635 186 48040.952700 812.036160 4.63e-177 1.000000 K80+I 23839.14050 184 48046.281000 817.364460 3.22e-178 1.000000 TPM3+I 23840.33241 185 48050.664820 821.748280 3.60e-179 1.000000 TPM1+I 23840.51044 185 48051.020880 822.104340 3.01e-179 1.000000 TVMef+I 23838.80284 187 48051.605680 822.689140 2.25e-179 1.000000 TPM2+I 23841.68566 185 48053.371320 824.454780 9.31e-180 1.000000 F81+I 23861.17445 186 48094.348900 865.432360 1.18e-188 1.000000 JC+I+G 23866.18876 184 48100.377520 871.460980 5.77e-190 1.000000 JC+G 23941.61114 183 48249.222280 1020.305740 0.00e+000 1.000000 JC+I 24052.33925 183 48470.678500 1241.761960 0.00e+000 1.000000 GTR 24458.75526 190 49297.510520 2068.593980 0.00e+000 1.000000 TIM2 24473.95929 188 49323.918580 2095.002040 0.00e+000 1.000000 TVM 24478.34797 189 49334.695940 2105.779400 0.00e+000 1.000000 TIM3 24491.63255 188 49359.265100 2130.348560 0.00e+000 1.000000 TPM2uf 24493.12170 187 49360.243400 2131.326860 0.00e+000 1.000000 TIM1 24498.52661 188 49373.053220 2144.136680 0.00e+000 1.000000 TrN 24500.61984 187 49375.239680 2146.323140 0.00e+000 1.000000 TPM3uf 24512.29253 187 49398.585060 2169.668520 0.00e+000 1.000000 TPM1uf 24513.91211 187 49401.824220 2172.907680 0.00e+000 1.000000 HKY 24525.76942 186 49423.538840 2194.622300 0.00e+000 1.000000 TIM2ef 24751.98477 185 49873.969540 2645.053000 0.00e+000 1.000000 SYM 24750.84925 187 49875.698500 2646.781960 0.00e+000 1.000000 TrNef 24756.34142 184 49880.682840 2651.766300 0.00e+000 1.000000 F81 24755.75973 185 49881.519460 2652.602920 0.00e+000 1.000000 TIM1ef 24758.16480 185 49886.329600 2657.413060 0.00e+000 1.000000 TIM3ef 24758.84663 185 49887.693260 2658.776720 0.00e+000 1.000000 TPM2 24773.80249 184 49915.604980 2686.688440 0.00e+000 1.000000 TPM1 24774.58826 184 49917.176520 2688.259980 0.00e+000 1.000000 TVMef 24772.66370 186 49917.327400 2688.410860 0.00e+000 1.000000 TPM3 24777.83987 184 49923.679740 2694.763200 0.00e+000 1.000000 K80 24780.90036 183 49927.800720 2698.884180 0.00e+000 1.000000 JC 24978.91320 182 50321.826400 3092.909860 0.00e+000 1.000000 ------------------------------------------------------------------------- -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: [ GTR+I+G TIM2+I+G TVM+I+G TPM2uf+I+G TIM3+I+G TIM1+I+G TrN+I+G TPM1uf+I+G TPM3uf+I+G HKY+I+G GTR+G TIM2+G TVM+G TPM2uf+G TIM3+G TIM1+G TrN+G TPM3uf+G TPM1uf+G HKY+G GTR+I TIM2+I TVM+I TPM2uf+I TIM1+I TIM3+I TrN+I TPM1uf+I TPM3uf+I HKY+I TIM3ef+I+G SYM+I+G TIM1ef+I+G TrNef+I+G TIM2ef+I+G TPM3+I+G TVMef+I+G TPM1+I+G K80+I+G TPM2+I+G F81+I+G TIM3ef+G TIM1ef+G TrNef+G SYM+G TIM2ef+G F81+G TPM3+G TPM1+G K80+G TVMef+G TPM2+G TIM2ef+I SYM+I TrNef+I TIM3ef+I TIM1ef+I K80+I TPM3+I TPM1+I TVMef+I TPM2+I F81+I JC+I+G JC+G JC+I GTR TIM2 TVM TIM3 TPM2uf TIM1 TrN TPM3uf TPM1uf HKY TIM2ef SYM TrNef F81 TIM1ef TIM3ef TPM2 TPM1 TVMef TPM3 K80 JC ] * AIC MODEL SELECTION : Parameter importance Parameter Importance ---------------------- fA 1.0000 fC 1.0000 fG 1.0000 fT 1.0000 kappa 0.0000 titv 0.0000 rAC 1.0000 rAG 1.0000 rAT 1.0000 rCG 0.9953 rCT 1.0000 rGT 1.0000 pinv(I) 0.0000 alpha(G) 0.0000 pinv(IG) 1.0000 alpha(IG) 1.0000 ---------------------- 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/jmodeltest1785295044061679662.phy -d nt -n 1 -b 0 --run_id GTR+I+G -m 012345 -f m -v e -c 4 -a e --no_memory_check -o tlr -s NNI --------------------------------------------------------------- * * * MODEL AVERAGED PHYLOGENY * * * --------------------------------------------------------------- Selection criterion: . . . . AIC Confidence interval: . . . . 1.00 Consensus type:. . . . . . . 50% majority rule Using 88 models in the 1.00 confidence interval = GTR+I+G TIM2+I+G TVM+I+G TPM2uf+I+G TIM3+I+G TIM1+I+G TrN+I+G TPM1uf+I+G TPM3uf+I+G HKY+I+G GTR+G TIM2+G TVM+G TPM2uf+G TIM3+G TIM1+G TrN+G TPM3uf+G TPM1uf+G HKY+G GTR+I TIM2+I TVM+I TPM2uf+I TIM1+I TIM3+I TrN+I TPM1uf+I TPM3uf+I HKY+I TIM3ef+I+G SYM+I+G TIM1ef+I+G TrNef+I+G TIM2ef+I+G TPM3+I+G TVMef+I+G TPM1+I+G K80+I+G TPM2+I+G F81+I+G TIM3ef+G TIM1ef+G TrNef+G SYM+G TIM2ef+G F81+G TPM3+G TPM1+G K80+G TVMef+G TPM2+G TIM2ef+I SYM+I TrNef+I TIM3ef+I TIM1ef+I K80+I TPM3+I TPM1+I TVMef+I TPM2+I F81+I JC+I+G JC+G JC+I GTR TIM2 TVM TIM3 TPM2uf TIM1 TrN TPM3uf TPM1uf HKY TIM2ef SYM TrNef F81 TIM1ef TIM3ef TPM2 TPM1 TVMef TPM3 K80 JC Species in order: 1. Circaea_alpina_GB 2. Circaea_lutetiana_GB 3. Fuchsia_cylindracea_F2 4. Fuchsia_glazioviana_F3_nocontig 5. Fuchsia_lycioides_F4 6. Hauya_heydeana_GB 7. L_ovalis_L3_4X 8. L_linearis_L16_2X 9. L_linifolia_L9_2X 10. L_curtisii_L27_8X 11. L_alata_L19_6X 12. L_repens_L25_6X 13. L_repens_L42_6X 14. L_arcuata_L38_4X 15. L_brevipes_L40_6X 16. L_spathulata_L39_4X 17. L_microcarpa_L13_2X 18. L_microcarpa_L22_2X 19. L_polycarpa_L37_4X 20. L_palustris_L26_2X 21. L_palustris_L41_2X 22. L_sphaerocarpa_L18_4X 23. L_glandulosa_L21_4X 24. L_suffruticosa_L20_4X 25. L_ravenii_L34_4X 26. L_lanceolata_L17_4X 27. L_pilosa_L28_4X 28. L_alternifolia_L10_2X 29. L_hirtella_L12_2X 30. L_maritima_L15_2X 31. L_virgata_L11_2X 32. L_torulosa_L132 33. L_hexapetala_L2_10X 34. L_grandiflora_L104_6XP 35. L_grandiflora_L108_6XP 36. L_peploides_L79_2X 37. L_peploides_L8_2X 38. L_stolonifera_L66_4X 39. L_x_taiwanensis_L96_3X 40. L_x_taiwanensis_L36_3X 41. L_adscendens_L93_4X 42. L_abyssinica_L65_6X 43. L_stenorraphe_L51_12X 44. L_stenorraphe_L52_12X 45. L_jussiaeoides_L33_M_8X 46. L_hyssopifolia_L71_2X 47. L_hyssopifolia_L32_M_2X 48. L_hyssopifolia_L73_2X 49. L_quadrangularis_L129 50. L_peruviana_L23_4X5X6X8X 51. L_leptocarpa_L102_4X6X 52. L_leptocarpa_L97_4X6X 53. L_leptocarpa_L76_4X6X 54. L_leptocarpa_L43_4X6X 55. L_leptocarpa_L49_4X6X 56. L_rigida_L133_ 57. L_pseudonarcissus_L111_4X 58. L_pseudonarcissus_L128_4X 59. L_perennis_L116_2X 60. L_perennis_L68_2X 61. L_martii_L113_6X 62. L_irwinii_L114_6X 63. L_myrtifolia_L115_6X 64. L_sericea_L100_4X 65. L_sericea_L101_4X 66. L_sericea_L112_4X 67. L_hassleriana_L107_4X 68. L_elegans_L109_8X 69. L_elegans_L103_8X 70. L_peruviana_L77_4X5X6X8X 71. L_decurrens_L98_2X 72. L_decurrens_L24_2X 73. L_decurrens_L82_2X 74. L_sedoides_L7_2X 75. L_inclinata_L120_2X 76. L_major_L99_2X 77. L_erecta_L44_2X 78. L_erecta_L95_2X 79. L_nervosa_L106_2X 80. L_nervosa_L110 81. L_bonariensis_L35_2X 82. L_octovalvis_L54_2X 83. L_octovalvis_L55_2X 84. L_neograndiflora_L105 85. L_neograndiflora_L59 86. L_lagunae_L58_2X 87. L_bonariensis_L56_2X 88. L_lagunae_L61_2X 89. L_octovalvis_L53_4X 90. L_octovalvis_L50_4X 91. L_octovalvis_L69_6X 92. L_octovalvis_L62_4X Bipartitions included in the consensus tree 12345678911111111112222222222333333333344444444445555555555666666666677777777778888888888999 01234567890123456789012345678901234567890123456789012345678901234567890123456789012 ******************************************************************************************** ( 1.0 ) --****************************************************************************************** ( 1.0 ) --***--------------------------------------------------------------------------------------- ( 1.0 ) ---**--------------------------------------------------------------------------------------- ( 1.0 ) -----*************************************************************************************** ( 1.0 ) ------************************************************************************************** ( 1.0 ) ------*************************------------------------------------------------------------- ( 1.0 ) ------*********************----------------------------------------------------------------- ( 1.0 ) -------********************----------------------------------------------------------------- ( 1.0 ) -------**----------------------------------------------------------------------------------- ( 1.0 ) ---------******************----------------------------------------------------------------- ( 1.0 ) ---------*********-------------------------------------------------------------------------- ( 1.0 ) ---------******----------------------------------------------------------------------------- ( 1.0 ) ----------*****----------------------------------------------------------------------------- ( 1.0 ) -----------****----------------------------------------------------------------------------- ( 1.0 ) -----------**------------------------------------------------------------------------------- ( 1.0 ) 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-----------------------------------------------------------------------------------------*** ( 1.0 ) ------------------------------------------------------------------------------------------** ( 1.0 ) +--92 L_grandiflora_L108_6XP +-174 | +--91 L_grandiflora_L104_6XP +-175 | +--90 L_hexapetala_L2_10X +-176 | | +--89 L_peploides_L8_2X | | +-172 | | | +--88 L_peploides_L79_2X | +-173 | | +--87 L_adscendens_L93_4X | | +-169 | | | +--86 L_x_taiwanensis_L36_3X | | +-170 | | | +--85 L_x_taiwanensis_L96_3X | +-171 | +--84 L_stolonifera_L66_4X +-177 | +--83 L_torulosa_L132 +-178 | | +--82 L_peruviana_L77_4X5X6X8X | | +-161 | | | +--81 L_elegans_L103_8X | | +-162 | | | +--80 L_elegans_L109_8X | | +-163 | | | | +--79 L_sericea_L101_4X | | | | +-158 | | | | | +--78 L_sericea_L100_4X | | | | +-159 | | | | | | +--77 L_hassleriana_L107_4X | | | | | +-157 | | | | | +--76 L_sericea_L112_4X | | | +-160 | | | | +--75 L_myrtifolia_L115_6X | | | +-156 | | | +--74 L_irwinii_L114_6X | | +-164 | | | +--73 L_martii_L113_6X | | +-165 | | | | +--72 L_major_L99_2X | | | | +-153 | | | | | +--------71 L_inclinata_L120_2X | | | | +-154 | | | | | +--70 L_sedoides_L7_2X | | | +-155 | | | | +--69 L_decurrens_L82_2X | | | | +-151 | | | | | +--68 L_decurrens_L24_2X | | | +-152 | | | +--67 L_decurrens_L98_2X | | +-166 | | | | +--66 L_erecta_L95_2X | | | | +-148 | | | | | +--65 L_erecta_L44_2X | | | | +-149 | | | | | | +--64 L_nervosa_L110 | | | | | +-147 | | | | | +--63 L_nervosa_L106_2X | | | +-150 | | | | +--62 L_octovalvis_L55_2X | | | | +-143 | | | | | +--61 L_octovalvis_L54_2X | | | | +-144 | | | | | | +--60 L_lagunae_L61_2X | | | | | | +-140 | | | | | | | +--59 L_bonariensis_L56_2X | | | | | | +-141 | | | | | | | +--58 L_lagunae_L58_2X | | | | | +-142 | | | | | | +--57 L_neograndiflora_L59 | | | | | +-139 | | | | | +--56 L_neograndiflora_L105 | | | | +-145 | | | | | +--55 L_bonariensis_L35_2X | | | +-146 | | | | +--54 L_octovalvis_L62_4X | | | | +-136 | | | | | +--53 L_octovalvis_L69_6X | | | | +-137 | | | | | +--52 L_octovalvis_L50_4X | | | +-138 | | | +--51 L_octovalvis_L53_4X | | +-167 | | | | +--50 L_perennis_L68_2X | | | +-135 | | | +--49 L_perennis_L116_2X | +-168 | | +--48 L_hyssopifolia_L73_2X | | +-130 | | | +--47 L_hyssopifolia_L32_M_2X | | +-131 | | | +--46 L_hyssopifolia_L71_2X | | +-132 | | | +--45 L_jussiaeoides_L33_M_8X | | +-133 | | | | +--44 L_stenorraphe_L52_12X | | | | +-128 | | | | | +--43 L_stenorraphe_L51_12X | | | +-129 | | | +--42 L_abyssinica_L65_6X | +-134 | | +--41 L_leptocarpa_L49_4X6X | | +-122 | | | +--40 L_leptocarpa_L43_4X6X | | +-123 | | | +--39 L_leptocarpa_L76_4X6X | | +-124 | | | | +--38 L_leptocarpa_L97_4X6X | | | +-121 | | | +--37 L_leptocarpa_L102_4X6X | | +-125 | | | | +--36 L_pseudonarcissus_L128_4X | | | | +-119 | | | | | +--35 L_pseudonarcissus_L111_4X | | | +-120 | | | +--34 L_rigida_L133_ | | +-126 | | | +--33 L_peruviana_L23_4X5X6X8X | +-127 | +--32 L_quadrangularis_L129 +----------------179 | | +--31 L_hirtella_L12_2X | | +-116 | | | +--30 L_alternifolia_L10_2X | | +-117 | | | | +--29 L_virgata_L11_2X | | | +-115 | | | +--28 L_maritima_L15_2X | +-118 | | +--27 L_microcarpa_L22_2X | | +-109 | | | +--26 L_microcarpa_L13_2X | | +-110 | | | +--25 L_spathulata_L39_4X | | +-111 | | | | +--24 L_brevipes_L40_6X | | | | +-105 | | | | | +--23 L_arcuata_L38_4X | | | | +-106 | | | | | | +--22 L_repens_L42_6X | | | | | +-104 | | | | | +--21 L_repens_L25_6X | | | | +-107 | | | | | +--20 L_alata_L19_6X | | | +-108 | | | +--19 L_curtisii_L27_8X | | +-112 | | | | +--18 L_pilosa_L28_4X | | | | +--98 | | | | | +--17 L_lanceolata_L17_4X | | | | +--99 | | | | | +--16 L_ravenii_L34_4X | | | | +-100 | | | | | +--15 L_suffruticosa_L20_4X | | | | +-101 | | | | | +--14 L_glandulosa_L21_4X | | | | +-102 | | | | | +--13 L_sphaerocarpa_L18_4X | | | +-103 | | | | +--12 L_palustris_L41_2X | | | | +--96 | | | | | +--11 L_palustris_L26_2X | | | +--97 | | | +--10 L_polycarpa_L37_4X | | +-113 | | | | +---9 L_linifolia_L9_2X | | | +--95 | | | +---8 L_linearis_L16_2X | +-114 | +---7 L_ovalis_L3_4X +--180 | +----6 Hauya_heydeana_GB +-181 | | +---5 Fuchsia_lycioides_F4 | | +--93 | | | +---4 Fuchsia_glazioviana_F3_nocontig | +--94 | +---3 Fuchsia_cylindracea_F2 | +---2 Circaea_lutetiana_GB | +---1 Circaea_alpina_GB (Circaea_alpina_GB:0.007780,Circaea_lutetiana_GB:0.002045,((Fuchsia_cylindracea_F2:0.015458,(Fuchsia_glazioviana_F3_nocontig:0.007167,Fuchsia_lycioides_F4:0.005328)1.00:0.004705)1.00:0.006106,(Hauya_heydeana_GB:0.021233,(((L_ovalis_L3_4X:0.005939,((L_linearis_L16_2X:0.003472,L_linifolia_L9_2X:0.004218)1.00:0.004695,(((L_polycarpa_L37_4X:0.002882,(L_palustris_L26_2X:0.000986,L_palustris_L41_2X:0.000631)1.00:0.000492)1.00:0.001490,(L_sphaerocarpa_L18_4X:0.003632,(L_glandulosa_L21_4X:0.001271,(L_suffruticosa_L20_4X:0.004833,(L_ravenii_L34_4X:0.002318,(L_lanceolata_L17_4X:0.011388,L_pilosa_L28_4X:0.001799)1.00:0.000000)1.00:0.001256)1.00:0.000712)1.00:0.000235)1.00:0.000762)1.00:0.001006,((L_curtisii_L27_8X:0.002314,(L_alata_L19_6X:0.001917,((L_repens_L25_6X:0.000000,L_repens_L42_6X:0.000000)1.00:0.001236,(L_arcuata_L38_4X:0.001259,L_brevipes_L40_6X:0.000000)1.00:0.002435)1.00:0.001745)1.00:0.001384)1.00:0.000682,(L_spathulata_L39_4X:0.002096,(L_microcarpa_L13_2X:0.000236,L_microcarpa_L22_2X:0.000492)1.00:0.003646)1.00:0.000000)1.00:0.000467)1.00:0.001011)1.00:0.000751)1.00:0.003978,((L_maritima_L15_2X:0.008167,L_virgata_L11_2X:0.004870)1.00:0.002060,(L_alternifolia_L10_2X:0.001936,L_hirtella_L12_2X:0.002525)1.00:0.002397)1.00:0.005437)1.00:0.009982,((((L_quadrangularis_L129:0.009739,(L_peruviana_L23_4X5X6X8X:0.010411,((L_rigida_L133_:0.002961,(L_pseudonarcissus_L111_4X:0.000715,L_pseudonarcissus_L128_4X:0.001381)1.00:0.000404)1.00:0.000791,((L_leptocarpa_L102_4X6X:0.002730,L_leptocarpa_L97_4X6X:0.002300)1.00:0.001509,(L_leptocarpa_L76_4X6X:0.000592,(L_leptocarpa_L43_4X6X:0.000000,L_leptocarpa_L49_4X6X:0.000631)1.00:0.000946)1.00:0.001340)1.00:0.005419)1.00:0.002900)1.00:0.001348)1.00:0.000812,((L_abyssinica_L65_6X:0.007486,(L_stenorraphe_L51_12X:0.002205,L_stenorraphe_L52_12X:0.002952)1.00:0.004897)1.00:0.002684,(L_jussiaeoides_L33_M_8X:0.011993,(L_hyssopifolia_L71_2X:0.002758,(L_hyssopifolia_L32_M_2X:0.002864,L_hyssopifolia_L73_2X:0.000000)1.00:0.000161)1.00:0.004906)1.00:0.003058)1.00:0.002241)1.00:0.004463,((L_perennis_L116_2X:0.000477,L_perennis_L68_2X:0.002183)1.00:0.016108,((((L_octovalvis_L53_4X:0.001952,(L_octovalvis_L50_4X:0.002743,(L_octovalvis_L69_6X:0.001310,L_octovalvis_L62_4X:0.000000)1.00:0.000000)1.00:0.000958)1.00:0.000683,(L_bonariensis_L35_2X:0.003291,(((L_neograndiflora_L105:0.004430,L_neograndiflora_L59:0.005576)1.00:0.001184,(L_lagunae_L58_2X:0.002816,(L_bonariensis_L56_2X:0.000344,L_lagunae_L61_2X:0.001722)1.00:0.002578)1.00:0.000753)1.00:0.000624,(L_octovalvis_L54_2X:0.003601,L_octovalvis_L55_2X:0.000572)1.00:0.001555)1.00:0.001605)1.00:0.000581)1.00:0.004177,((L_nervosa_L106_2X:0.000000,L_nervosa_L110:0.000494)1.00:0.004321,(L_erecta_L44_2X:0.000748,L_erecta_L95_2X:0.000748)1.00:0.006779)1.00:0.005122)1.00:0.000341,(((L_decurrens_L98_2X:0.000264,(L_decurrens_L24_2X:0.000000,L_decurrens_L82_2X:0.000000)1.00:0.000285)1.00:0.007274,(L_sedoides_L7_2X:0.014304,(L_inclinata_L120_2X:0.040629,L_major_L99_2X:0.006732)1.00:0.002290)1.00:0.001071)1.00:0.000260,(L_martii_L113_6X:0.008380,(((L_irwinii_L114_6X:0.013346,L_myrtifolia_L115_6X:0.003711)1.00:0.004403,((L_sericea_L112_4X:0.004703,L_hassleriana_L107_4X:0.008344)1.00:0.001239,(L_sericea_L100_4X:0.001537,L_sericea_L101_4X:0.002339)1.00:0.000646)1.00:0.001204)1.00:0.001644,(L_elegans_L109_8X:0.003533,(L_elegans_L103_8X:0.001899,L_peruviana_L77_4X5X6X8X:0.005990)1.00:0.013713)1.00:0.001621)1.00:0.000780)1.00:0.001589)1.00:0.001441)1.00:0.004321)1.00:0.000620)1.00:0.001794,(L_torulosa_L132:0.013685,(((L_stolonifera_L66_4X:0.003808,(L_x_taiwanensis_L96_3X:0.000726,(L_x_taiwanensis_L36_3X:0.000713,L_adscendens_L93_4X:0.001916)1.00:0.000695)1.00:0.003519)1.00:0.001474,(L_peploides_L79_2X:0.002599,L_peploides_L8_2X:0.002298)1.00:0.001304)1.00:0.000420,(L_hexapetala_L2_10X:0.000000,(L_grandiflora_L104_6XP:0.000226,L_grandiflora_L108_6XP:0.000917)1.00:0.000521)1.00:0.001431)1.00:0.008224)1.00:0.003404)1.00:0.004993)1.00:0.077335)1.00:0.023126)1.00:0.016943); 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) --------------------------------------------------------------- * * * SELECTION SUMMARY * * * --------------------------------------------------------------- ::Optimized Topologies Summary:: There are 21 different topologies. Topology Id: 1 Rank Weight RF AvgEucl VarEucl AIC 1 100.00% 0 6.05e-04 1.71e-07 Models supporting: 4 TPM2uf+I+G TIM2+I+G TVM+I+G GTR+I+G Topology Id: 2 Rank Weight RF AvgEucl VarEucl AIC 2 0.00% 2 6.81e-02 1.20e-06 Models supporting: 2 TIM1+I+G TIM3+I+G Topology Id: 3 Rank Weight RF AvgEucl VarEucl AIC 3 0.00% 4 3.84e-02 8.33e-04 Models supporting: 2 TrN+I+G TPM1uf+I+G Topology Id: 4 Rank Weight RF AvgEucl VarEucl AIC 4 0.00% 8 7.40e-02 0.00e+00 Models supporting: 1 TPM3uf+I+G Topology Id: 5 Rank Weight RF AvgEucl VarEucl AIC 5 0.00% 12 7.04e-02 1.11e-09 Models supporting: 3 K80+I+G HKY+I+G TPM2+I+G Topology Id: 6 Rank Weight RF AvgEucl VarEucl AIC 6 0.00% 12 6.94e-02 0.00e+00 Models supporting: 1 SYM+I+G Topology Id: 7 Rank Weight RF AvgEucl VarEucl AIC 7 0.00% 14 7.03e-02 4.00e-08 Models supporting: 9 JC+I+G F81+I+G TrNef+I+G TPM1+I+G TPM3+I+G TIM1ef+I+G TIM2ef+I+G TIM3ef+I+G TVMef+I+G Topology Id: 8 Rank Weight RF AvgEucl VarEucl AIC 8 0.00% 16 6.63e-02 1.32e-06 Models supporting: 2 K80+I TIM2ef+I Topology Id: 9 Rank Weight RF AvgEucl VarEucl AIC 9 0.00% 16 7.34e-02 1.76e-09 Models supporting: 4 K80+G TIM1ef+G TIM2ef+G TIM3ef+G Topology Id: 10 Rank Weight RF AvgEucl VarEucl AIC 10 0.00% 18 7.69e-02 0.00e+00 Models supporting: 1 JC+G Topology Id: 11 Rank Weight RF AvgEucl VarEucl AIC 11 0.00% 18 7.34e-02 1.30e-06 Models supporting: 22 HKY+G TrNef TrNef+G TrN TrN+G TPM1 TPM1+G TPM1uf TPM1uf+G TPM2+G TPM2uf+G TPM3+G TPM3uf+G TIM1+G TIM2ef TIM2+G TIM3+G TVMef+G TVM+G SYM SYM+G GTR+G Topology Id: 12 Rank Weight RF AvgEucl VarEucl AIC 12 0.00% 18 6.91e-02 0.00e+00 Models supporting: 1 TIM3ef+I Topology Id: 13 Rank Weight RF AvgEucl VarEucl AIC 13 0.00% 20 6.82e-02 0.00e+00 Models supporting: 1 JC+I Topology Id: 14 Rank Weight RF AvgEucl VarEucl AIC 14 0.00% 20 7.27e-02 0.00e+00 Models supporting: 1 F81+G Topology Id: 15 Rank Weight RF AvgEucl VarEucl AIC 15 0.00% 20 6.92e-02 0.00e+00 Models supporting: 1 TIM1ef+I Topology Id: 16 Rank Weight RF AvgEucl VarEucl AIC 16 0.00% 22 7.64e-02 3.02e-06 Models supporting: 2 JC K80 Topology Id: 17 Rank Weight RF AvgEucl VarEucl AIC 17 0.00% 22 6.99e-02 3.02e-08 Models supporting: 9 TrNef+I TrN+I TPM1+I TPM2+I TPM3+I TPM3uf+I TIM3+I TVMef+I SYM+I Topology Id: 18 Rank Weight RF AvgEucl VarEucl AIC 18 0.00% 22 7.36e-02 3.77e-11 Models supporting: 4 TPM2uf TIM2 TVM GTR Topology Id: 19 Rank Weight RF AvgEucl VarEucl AIC 19 0.00% 24 6.88e-02 1.47e-06 Models supporting: 8 F81+I HKY+I TPM1uf+I TPM2uf+I TIM1+I TIM2+I TVM+I GTR+I Topology Id: 20 Rank Weight RF AvgEucl VarEucl AIC 20 0.00% 24 7.44e-02 6.01e-07 Models supporting: 7 TPM2 TPM3 TPM3uf TIM1ef TIM3ef TIM3 TVMef Topology Id: 21 Rank Weight RF AvgEucl VarEucl AIC 21 0.00% 26 7.30e-02 4.90e-07 Models supporting: 3 F81 HKY TIM1 ::Best Models:: Model f(a) f(c) f(g) f(t) kappa titv Ra Rb Rc Rd Re Rf pInv gamma ---------------------------------------------------------------------------------------------------------------------------------------- AIC GTR+I+G 0.34 0.19 0.18 0.30 0.00 0.00 0.783 1.659 0.550 1.137 2.236 1.000 0.51 0.74