-------------------------- jModeltest 2.1.7 v20141120 -------------------------- (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 -------------------------------------------------------------------------------- Sat Jun 03 16:27:05 IDT 2017 Linux 2.6.32-504.12.2.el6.x86_64, arch: amd64, bits: 64, numcores: 48 -------------------------------------------------------------------------------- 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 2.1.7 v20141120 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 = -d /bioseq/data/results/ConSurf/1496496375/ModelTest//input_msa.phy -t BIONJ -AICc -f -o model_selection_out.txt Reading data file "input_msa.phy"... OK. number of sequences: 487 number of sites: 191 --------------------------------------------------------------- * * * COMPUTATION OF LIKELIHOOD SCORES WITH PHYML * * * --------------------------------------------------------------- ::Settings:: Phyml version = 3.0 Phyml binary = PhyML_3.0_linux64 Phyml path = /bioseq/Programs/ModelTest/jmodeltest-2.1.7/exe/phyml/ Candidate models = 6 number of substitution schemes = 3 including models with equal/unequal base frequencies (+F) including only models without a proportion of invariable sites including only models without rate variation among sites Optimized free parameters (K) = substitution parameters + 971 branch lengths Base tree for likelihood calculations = BIONJ tree ::Progress:: Model Exec. Time Total Time -lnL ------------------------------------------------------------------------- JC 00h:00:30:01 00h:00:30:01 31853.8623 (1/6) SYM 00h:00:35:06 00h:00:35:06 31144.0800 (2/6) K80 00h:00:36:05 00h:00:36:05 31218.0887 (3/6) F81 00h:00:36:09 00h:00:36:09 31768.2839 (4/6) HKY 00h:00:43:09 00h:00:43:09 31085.1959 (5/6) GTR 00h:00:53:02 00h:00:53:02 31058.8810 (6/6) Model = JC partition = 000000 -lnL = 31853.8623 K = 971 Model = F81 partition = 000000 -lnL = 31768.2839 K = 974 freqA = 0.2866 freqC = 0.1933 freqG = 0.2138 freqT = 0.3063 Model = K80 partition = 010010 -lnL = 31218.0887 K = 972 kappa = 2.5635 (ti/tv = 1.2817) Model = HKY partition = 010010 -lnL = 31085.1959 K = 975 freqA = 0.2812 freqC = 0.1913 freqG = 0.2094 freqT = 0.3181 kappa = 2.6431 (ti/tv = 1.2663) Model = SYM partition = 012345 -lnL = 31144.0800 K = 976 R(a) [AC] = 0.7186 R(b) [AG] = 2.6679 R(c) [AT] = 1.5270 R(d) [CG] = 0.9392 R(e) [CT] = 2.7512 R(f) [GT] = 1.0000 Model = GTR partition = 012345 -lnL = 31058.8810 K = 979 freqA = 0.3031 freqC = 0.1806 freqG = 0.2010 freqT = 0.3154 R(a) [AC] = 0.7880 R(b) [AG] = 2.6487 R(c) [AT] = 1.0730 R(d) [CG] = 1.4094 R(e) [CT] = 2.9361 R(f) [GT] = 1.0000 Best-fit models should be reoptimized for comparison with unconstrained likelihood Computation of likelihood scores completed. It took 00h:00:53:02. --------------------------------------------------------------- * * * CORRECTED AKAIKE INFORMATION CRITERION (AICc) * * * --------------------------------------------------------------- Sample size: 191.0 Model selected: Model = GTR partition = 012345 -lnL = 31058.8810 K = 979 freqA = 0.3031 freqC = 0.1806 freqG = 0.2010 freqT = 0.3154 R(a) [AC] = 0.7880 R(b) [AG] = 2.6487 R(c) [AT] = 1.0730 R(d) [CG] = 1.4094 R(e) [CT] = 2.9361 R(f) [GT] = 1.0000 Tree for the best AICc model = 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* AICc MODEL SELECTION : Selection uncertainty Model -lnL K AICc delta weight cumWeight ------------------------------------------------------------------------- GTR 31058.88100 979 61643.772139 0.000000 1.000000 1.000000 HKY 31085.19591 975 61695.933221 52.161082 4.71e-012 1.000000 SYM 31144.07997 976 61813.818973 170.046834 1.19e-037 1.000000 K80 31218.08871 972 61961.364121 317.591981 1.09e-069 1.000000 F81 31768.28391 974 63061.991289 1418.219150 0.00e+000 1.000000 JC 31853.86232 971 63232.792502 1589.020362 0.00e+000 1.000000 ------------------------------------------------------------------------- -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 6 models in the 100% confidence interval: [ GTR HKY SYM K80 F81 JC ] * AICc MODEL SELECTION : Best Model's command line phyml -i /tmp/jmodeltest6013390128390688581.phy -d nt -n 1 -b 0 --run_id GTR -m 012345 -f m -c 1 --no_memory_check -o lr --------------------------------------------------------------- * * * SELECTION SUMMARY * * * --------------------------------------------------------------- ::Optimized Topologies Summary:: There are 2 different topologies. Topology Id: 1 Rank Weight RF AvgEucl VarEucl AICc 1 100.00% 0 4.43e-01 1.40e-01 Models supporting: 3 F81 HKY GTR Topology Id: 2 Rank Weight RF AvgEucl VarEucl AICc 2 0.00% 316 4.34e+00 2.15e-03 Models supporting: 3 JC K80 SYM ::Best Models:: Model f(a) f(c) f(g) f(t) kappa titv Ra Rb Rc Rd Re Rf pInv gamma ---------------------------------------------------------------------------------------------------------------------------------------- AICc GTR 0.30 0.18 0.20 0.32 0.00 0.00 0.788 2.649 1.073 1.409 2.936 1.000 N/A N/A