ProtTest 3.4.1 Fast selection of the best-fit models of protein evolution (c) 2009-2010 Diego Darriba (1,2), Guillermo Taboada (2), Ramón Doallo (2), David Posada (1) (1) Facultad de Biologia, Universidad de Vigo, 36200 Vigo, Spain (2) Facultade de Informática, Universidade da Coruña, 15071 A Coruña, Spain Contact: ddarriba@udc.es, dposada@uvigo.es ---------------------------------------------------------------------------------------------- Sat Jun 03 16:29:07 IDT 2017 OS = Linux (2.6.32-504.12.2.el6.x86_64) Citation: Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27:1164-1165, 2011 ProtTest options ---------------- Alignment file........... : /bioseq/data/results/ConSurf/1496496145/ModelTest//input_msa.phy Tree..................... : BioNJ StrategyMode............. : BIONJ Tree Candidate models......... : Matrices............... : JTT LG MtREV Dayhoff WAG CpREV Distributions.......... : Uniform Observed frequencies... : false Statistical framework Sort models according to....: AICc Sample size.................: 331.0 (not calculated yet) Other options: Display best tree in ASCII..: false Display best tree in Newick.: false Display consensus tree......: false Verbose.....................: false ********************************************************** Observed number of invariant sites: 0 Observed aminoacid frequencies: A: 0.063 C: 0.017 D: 0.065 E: 0.084 F: 0.032 G: 0.077 H: 0.031 I: 0.030 K: 0.038 L: 0.075 M: 0.017 N: 0.028 P: 0.048 Q: 0.057 R: 0.074 S: 0.054 T: 0.068 V: 0.057 W: 0.033 Y: 0.052 ********************************************************** Model................................ : JTT Number of parameters............... : 297 (0 + 297 branch length estimates) -lnL................................ = 40102.25 (seconds)) Model................................ : LG Number of parameters............... : 297 (0 + 297 branch length estimates) -lnL................................ = 40792.63 (seconds)) Model................................ : MtREV Number of parameters............... : 297 (0 + 297 branch length estimates) -lnL................................ = 43610.53 (seconds)) Model................................ : Dayhoff Number of parameters............... : 297 (0 + 297 branch length estimates) -lnL................................ = 41249.62 (seconds)) Model................................ : WAG Number of parameters............... : 297 (0 + 297 branch length estimates) -lnL................................ = 40187.01 (seconds)) Model................................ : CpREV Number of parameters............... : 297 (0 + 297 branch length estimates) -lnL................................ = 40750.56 (seconds)) ************************************************************ Date : Sat Jun 03 16:29:55 IDT 2017 Runtime: 0h:00:48 *************************************************************************** Best model according to AICc: JTT Confidence Interval: 100.0 *************************************************************************** Model deltaAICc AICc AICcw -lnL --------------------------------------------------------------------------- JTT 0.00 86162.50 1.00 40102.25 WAG 169.52 86332.02 0.00 40187.01 CpREV 1296.61 87459.11 0.00 40750.56 LG 1380.76 87543.26 0.00 40792.63 Dayhoff 2294.75 88457.25 0.00 41249.62 MtREV 7016.55 93179.05 0.00 43610.53 --------------------------------------------------------------------------- --------------------------------------------------------------------------- *********************************************** Relative importance of parameters *********************************************** alpha (+G): No +G models p-inv (+I): No +I models alpha+p-inv (+I+G): No +I+G models freqs (+F): No +F models *********************************************** Model-averaged estimate of parameters *********************************************** alpha (+G): No +G models p-inv (+I): No +I models alpha (+I+G): No +I+G models p-inv (+I+G): No +I+G models