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 14:32:19 CET 2009 OS = Mac OS X (10.5.6) ProtTest options ---------------- Alignment file........... : /Users/budd/Desktop/Training/topicSpecificTrainingContent/phylogenies/analysisFromAtoZ//TF105399_seed_trimmed_HandGblocked_NameEd.phy Tree..................... : BioNJ StrategyMode............. : Fast (optimize branch lengths & model) Candidate models......... : Matrices............... : WAG JTT Distributions.......... : +I +G Observed frequencies... : true ********************************************************** Reading alignment... Sequence #1: DRM_CG4107 Sequence #2: AEDAE_0452 Sequence #3: CIOSA_1192 Sequence #4: CIOIN_3167 Sequence #5: XENTR_4922 Sequence #6: GASAC11546 Sequence #7: TETNG22052 Sequence #8: FUGRU17779 Sequence #9: RAT__55250 Sequence #10: CANFA24870 Sequence #11: MOUSE_6973 Sequence #12: HUMAN22591 Sequence #13: XENTR30583 Sequence #14: MONDO34106 Sequence #15: CHICK18402 Sequence #16: BOVIN_0994 Sequence #17: HUMAN26375 Sequence #18: GASAC_6611 Sequence #19: FUGRU15917 Alignment contains 19 sequences of length 507 ********************************************************** Observed number of invariant sites: 207 Observed aminoacid frequencies: A: 0.036 C: 0.026 D: 0.039 E: 0.078 F: 0.057 G: 0.042 H: 0.027 I: 0.065 K: 0.092 L: 0.100 M: 0.029 N: 0.032 P: 0.046 Q: 0.045 R: 0.067 S: 0.045 T: 0.052 V: 0.059 W: 0.010 Y: 0.053 ********************************************************** Model................................ : WAG Number of parameters............... : 35 (0 + 35 branch length estimates) -lnL................................ = 4897.69 (0h0m11s) Model................................ : WAG+F Number of parameters............... : 54 (19 + 35 branch length estimates) aminoacid frequencies............ = observed (see above) -lnL................................ = 4898.03 (0h0m6s) Model................................ : WAG+I Number of parameters............... : 36 (1 + 35 branch length estimates) proportion of invariable sites... = 0.299 -lnL................................ = 4843.61 (0h0m27s) Model................................ : WAG+I+F Number of parameters............... : 55 (20 + 35 branch length estimates) proportion of invariable sites... = 0.303 aminoacid frequencies............ = observed (see above) -lnL................................ = 4841.89 (0h0m27s) Model................................ : WAG+G Number of parameters............... : 36 (1 + 35 branch length estimates) gamma shape (4 rate categories).. = 0.984 -lnL................................ = 4833.90 (0h1m49s) Model................................ : WAG+G+F Number of parameters............... : 55 (20 + 35 branch length estimates) gamma shape (4 rate categories).. = 0.945 aminoacid frequencies............ = observed (see above) -lnL................................ = 4830.13 (0h1m45s) Model................................ : JTT Number of parameters............... : 35 (0 + 35 branch length estimates) -lnL................................ = 4835.55 (0h0m8s) Model................................ : JTT+F Number of parameters............... : 54 (19 + 35 branch length estimates) aminoacid frequencies............ = observed (see above) -lnL................................ = 4833.35 (0h0m7s) Model................................ : JTT+I Number of parameters............... : 36 (1 + 35 branch length estimates) proportion of invariable sites... = 0.306 -lnL................................ = 4776.99 (0h0m27s) Model................................ : JTT+I+F Number of parameters............... : 55 (20 + 35 branch length estimates) proportion of invariable sites... = 0.307 aminoacid frequencies............ = observed (see above) -lnL................................ = 4775.45 (0h0m25s) Model................................ : JTT+G Number of parameters............... : 36 (1 + 35 branch length estimates) gamma shape (4 rate categories).. = 0.964 -lnL................................ = 4770.15 (0h1m47s) Model................................ : JTT+G+F Number of parameters............... : 55 (20 + 35 branch length estimates) gamma shape (4 rate categories).. = 0.948 aminoacid frequencies............ = observed (see above) -lnL................................ = 4766.54 (0h1m55s) ************************************************************ Date : Sat Feb 07 14:42:01 CET 2009 Runtime: 0h:09:40 ************************************************************ Akaike Information Chriterion (AIC) framework ************************************************************ Best model according to AIC: JTT+G ************************************************************ Model deltaAIC* AIC AICw -lnL ------------------------------------------------------------ JTT+G 0.00 9612.30 1.00 -4770.15 JTT+I 13.68 9625.98 0.00 -4776.99 JTT+G+F 30.78 9643.08 0.00 -4766.54 JTT+I+F 48.60 9660.90 0.00 -4775.45 WAG+G 127.49 9739.79 0.00 -4833.90 JTT 128.80 9741.10 0.00 -4835.55 WAG+I 146.93 9759.23 0.00 -4843.61 WAG+G+F 157.96 9770.26 0.00 -4830.13 JTT+F 162.40 9774.70 0.00 -4833.35 WAG+I+F 181.49 9793.78 0.00 -4841.89 WAG 253.09 9865.39 0.00 -4897.69 WAG+F 291.77 9904.07 0.00 -4898.03 ------------------------------------------------------------ *: 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): 0.96 p-inv (+I): 0.31 alpha (+I+G): ? p-inv (+I+G): ? ************************************************************ Second-order AIC (AICc) framework Sample size: Total number of characters (aligment length) = 507.00 ************************************************************ Best model according to second-order AIC: JTT+G ************************************************************ Model deltaAICc* AICc AICcw -lnL ------------------------------------------------------------ JTT+G 0.00 9617.97 1.00 -4770.15 JTT+I 13.68 9631.64 0.00 -4776.99 JTT+G+F 38.77 9656.73 0.00 -4766.54 JTT+I+F 56.59 9674.56 0.00 -4775.45 WAG+G 127.49 9745.46 0.00 -4833.90 JTT 128.48 9746.45 0.00 -4835.55 WAG+I 146.93 9764.90 0.00 -4843.61 WAG+G+F 165.95 9783.92 0.00 -4830.13 JTT+F 169.87 9787.84 0.00 -4833.35 WAG+I+F 189.48 9807.44 0.00 -4841.89 WAG 252.77 9870.74 0.00 -4897.69 WAG+F 299.24 9917.21 0.00 -4898.03 ------------------------------------------------------------ *: models sorted according to this column ------------------------------------------------------------ sample size: 507.00 ------------------------------------------------------------ *********************************************** 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): 0.96 p-inv (+I): 0.31 alpha (+I+G): ? p-inv (+I+G): ? ************************************************************ Bayesian Information Chriterion (BIC) framework Sample size: Total number of characters (aligment length) = 507.00 ************************************************************ Best model according to BIC: JTT+G ************************************************************ Model deltaBIC* BIC BICw -lnL ------------------------------------------------------------ JTT+G 0.00 9764.52 1.00 -4770.15 JTT+I 13.68 9778.20 0.00 -4776.99 JTT+G+F 111.12 9875.64 0.00 -4766.54 JTT 124.57 9889.10 0.00 -4835.55 WAG+G 127.49 9892.02 0.00 -4833.90 JTT+I+F 128.94 9893.47 0.00 -4775.45 WAG+I 146.93 9911.46 0.00 -4843.61 WAG+G+F 238.30 10002.83 0.00 -4830.13 JTT+F 238.51 10003.04 0.00 -4833.35 WAG 248.86 10013.38 0.00 -4897.69 WAG+I+F 261.83 10026.35 0.00 -4841.89 WAG+F 367.88 10132.40 0.00 -4898.03 ------------------------------------------------------------ *: models sorted according to this column ------------------------------------------------------------ sample size: 507.00 ------------------------------------------------------------ *********************************************** 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): 0.96 p-inv (+I): 0.31 alpha (+I+G): ? p-inv (+I+G): ? *********************************************************** Results succesfully saved to: TF105399_seed_trimmed_HandGblocked_NameEd.phy.prottest *********************************************************** ---------------------------------------------------------------------------------------------------- Table: Weights(Ranking) of the candidate models under the different frameworks ---------------------------------------------------------------------------------------------------- model AIC AICc-1 AICc-2 AICc-3 BIC-1 BIC-2 BIC-3 JTT+G 1.00(1) 1.00(1) 1.00(1) 1.00(1) 1.00(1) 1.00(1) 1.00(1) JTT+I 0.00(2) 0.00(2) 0.00(2) 0.00(2) 0.00(2) 0.00(2) 0.00(2) JTT+G+F 0.00(3) 0.00(3) 0.00(3) 0.00(3) 0.00(3) 0.00(3) 0.00(4) JTT+I+F 0.00(4) 0.00(4) 0.00(4) 0.00(4) 0.00(6) 0.00(4) 0.00(6) WAG+G 0.00(5) 0.00(5) 0.00(5) 0.00(5) 0.00(5) 0.00(6) 0.00(5) JTT 0.00(6) 0.00(6) 0.00(6) 0.00(6) 0.00(4) 0.00(5) 0.00(3) WAG+I 0.00(7) 0.00(7) 0.00(7) 0.00(7) 0.00(7) 0.00(7) 0.00(7) WAG+G+F 0.00(8) 0.00(8) 0.00(8) 0.00(8) 0.00(8) 0.00(8) 0.00(10) JTT+F 0.00(9) 0.00(9) 0.00(9) 0.00(9) 0.00(9) 0.00(9) 0.00(9) WAG+I+F 0.00(10) 0.00(10) 0.00(10) 0.00(10) 0.00(11) 0.00(11) 0.00(11) WAG 0.00(11) 0.00(11) 0.00(11) 0.00(11) 0.00(10) 0.00(10) 0.00(8) WAG+F 0.00(12) 0.00(12) 0.00(12) 0.00(12) 0.00(12) 0.00(12) 0.00(12) ---------------------------------------------------------------------------------------------------- Relative importance of parameters AIC AICc-1 AICc-2 AICc-3 BIC-1 BIC-2 BIC-3 +G 1.00 1.00 1.00 1.00 1.00 1.00 1.00 +I 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +I+G 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +F 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ---------------------------------------------------------------------------------------------------- Model-averaged estimate of parameters AIC AICc-1 AICc-2 AICc-3 BIC-1 BIC-2 BIC-3 alpha (+G) 0.96 0.96 0.96 0.96 0.96 0.96 0.96 p-inv (+I) 0.31 0.31 0.31 0.31 0.31 0.31 0.31 alpha (+I+G) ? ? ? ? ? ? ? p-inv (+I+G) ? ? ? ? ? ? ? ---------------------------------------------------------------------------------------------------- AIC : Akaike Information Criterion framework. AICc-x: Second-Order Akaike framework. BIC-x : Bayesian Information Criterion framework. AICc/BIC-1: sample size as: number of sites in the alignment (507.0) AICc/BIC-2: sample size as: Sum of position's Shannon Entropy over the whole alignment (269.1) AICc/BIC-3: sample size as: align. length x num sequences x averaged (0-1)Sh. Entropy (1183.0) ----------------------------------------------------------------------------------------------------