ProtTest - 1.4 Selection of models of protein evolution (c) 2004 Federico Abascal, Rafael Zardoya, David Posada (FA, DP) Facultad de Biologia, Universidad de Vigo, 36200 Vigo, Spain (RZ) Museo Nacional de Ciencias Naturales, 28006 Madrid, Spain Contact: fabascal@uvigo.es, dposada@uvigo.es -------------------------------------------------------------------------------- Sat Feb 07 20:09:23 CET 2009 OS = Mac OS X (10.5.6) ProtTest options ---------------- Alignment file........... : /Users/budd/Desktop/Training/topicSpecificTrainingContent/phylogenies/analysisFromAtoZ//TF105907_full_trimmed_handGblocked_NameEd.phy Tree..................... : BioNJ StrategyMode............. : Fast (optimize branch lengths & model) Candidate models......... : Matrices............... : JTT WAG Distributions.......... : +G Observed frequencies... : true ********************************************************** Reading alignment... Sequence #1: ORYLA10739 Sequence #2: GASAC10739 Sequence #3: SCHMA7630a Sequence #4: SCHMA7630b Sequence #5: BRARE5631 Sequence #6: CHICK10739 Sequence #7: ORNAN10739 Sequence #8: BOVIN51668 Sequence #9: HUMAN10739 Sequence #10: MOUSEPABPa Sequence #11: XENTR_PABP Sequence #12: BRARE_PABP Sequence #13: ORYLA_PABP Sequence #14: GASAC_PABP Sequence #15: TETNG96340 Sequence #16: FUGRU_PABP Sequence #17: XENTRQ6NVP Sequence #18: BOVIN_PABP Sequence #19: HUMAN_PABP Sequence #20: MOUSE_PABP Alignment contains 20 sequences of length 109 ********************************************************** Observed number of invariant sites: 45 Observed aminoacid frequencies: A: 0.085 C: 0.019 D: 0.059 E: 0.099 F: 0.044 G: 0.077 H: 0.027 I: 0.064 K: 0.063 L: 0.054 M: 0.023 N: 0.033 P: 0.031 Q: 0.010 R: 0.075 S: 0.069 T: 0.060 V: 0.073 W: 0.001 Y: 0.034 ********************************************************** Model................................ : JTT Number of parameters............... : 37 (0 + 37 branch length estimates) -lnL................................ = 1365.76 (0h0m4s) Model................................ : JTT+F Number of parameters............... : 56 (19 + 37 branch length estimates) aminoacid frequencies............ = observed (see above) -lnL................................ = 1370.26 (0h0m3s) Model................................ : JTT+G Number of parameters............... : 38 (1 + 37 branch length estimates) gamma shape (4 rate categories).. = 0.525 -lnL................................ = 1306.34 (0h0m44s) Model................................ : JTT+G+F Number of parameters............... : 57 (20 + 37 branch length estimates) gamma shape (4 rate categories).. = 0.514 aminoacid frequencies............ = observed (see above) -lnL................................ = 1309.35 (0h0m46s) Model................................ : WAG Number of parameters............... : 37 (0 + 37 branch length estimates) -lnL................................ = 1368.86 (0h0m3s) Model................................ : WAG+F Number of parameters............... : 56 (19 + 37 branch length estimates) aminoacid frequencies............ = observed (see above) -lnL................................ = 1367.30 (0h0m2s) Model................................ : WAG+G Number of parameters............... : 38 (1 + 37 branch length estimates) gamma shape (4 rate categories).. = 0.566 -lnL................................ = 1315.08 (0h0m42s) Model................................ : WAG+G+F Number of parameters............... : 57 (20 + 37 branch length estimates) gamma shape (4 rate categories).. = 0.562 aminoacid frequencies............ = observed (see above) -lnL................................ = 1313.13 (0h0m40s) ************************************************************ Date : Sat Feb 07 20:21:59 CET 2009 Runtime: 0h:12:37 ************************************************************ Akaike Information Chriterion (AIC) framework ************************************************************ Best model according to AIC: JTT+G ************************************************************ Model deltaAIC* AIC AICw -lnL ------------------------------------------------------------ JTT+G 0.00 2688.68 1.00 -1306.34 WAG+G 17.47 2706.16 0.00 -1315.08 JTT+G+F 44.02 2732.71 0.00 -1309.35 WAG+G+F 51.58 2740.27 0.00 -1313.13 JTT 116.84 2805.52 0.00 -1365.76 WAG 123.04 2811.72 0.00 -1368.86 WAG+F 157.93 2846.61 0.00 -1367.30 JTT+F 163.83 2852.52 0.00 -1370.26 ------------------------------------------------------------ *: models sorted according to this column ------------------------------------------------------------ *********************************************** Relative importance of parameters *********************************************** alpha (+G): 1.00 p-inv (+I): 0.00 alpha+p-inv (+I+G): 0.00 freqs (+F): 0.00 *********************************************** Model-averaged estimate of parameters *********************************************** alpha (+G): 0.53 p-inv (+I): ? alpha (+I+G): ? p-inv (+I+G): ? ************************************************************ Bayesian Information Chriterion (BIC) framework Sample size: Total number of characters (aligment length) = 109.00 ************************************************************ Best model according to BIC: JTT+G ************************************************************ Model deltaBIC* BIC BICw -lnL ------------------------------------------------------------ JTT+G 0.00 2790.96 1.00 -1306.34 WAG+G 17.47 2808.43 0.00 -1315.08 JTT+G+F 95.16 2886.11 0.00 -1309.35 WAG+G+F 102.72 2893.67 0.00 -1313.13 JTT 114.14 2905.10 0.00 -1365.76 WAG 120.35 2911.30 0.00 -1368.86 WAG+F 206.37 2997.32 0.00 -1367.30 JTT+F 212.28 3003.23 0.00 -1370.26 ------------------------------------------------------------ *: models sorted according to this column ------------------------------------------------------------ sample size: 109.00 ------------------------------------------------------------ *********************************************** Relative importance of parameters *********************************************** alpha (+G): 1.00 p-inv (+I): 0.00 alpha+p-inv (+I+G): 0.00 freqs (+F): 0.00 *********************************************** Model-averaged estimate of parameters *********************************************** alpha (+G): 0.53 p-inv (+I): ? alpha (+I+G): ? p-inv (+I+G): ?