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ProtTest 3.4.2                      Fast selection of the best-fit models of protein evolution
(c) 2009-2016   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
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Manual:                                    http://darwin.uvigo.es/download/prottest_manual.pdf
Homepage:                                                 http://github.com/ddarriba/prottest3
Discussion group:                                     https://groups.google.com/group/prottest
Contact:                                                  ddarriba@h-its.org, dposada@uvigo.es
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Version:  3.4.2 : 8th May 2016
Date:     Wed Jan 08 05:08:39 IST 2025
OS:       Linux (5.14.0-427.26.1.el9_4.x86_64)
Arch:     amd64
Java:     17.0.12 (Red Hat, Inc.)
PhyML:    /bentallab/programs/prottest-3.4.2/bin/PhyML_3.0_linux64

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........... : 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.................: 301.0
  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: 1
Observed aminoacid frequencies:
 A: 0.063    C: 0.003    D: 0.084    E: 0.067    F: 0.035   
 G: 0.072    H: 0.015    I: 0.071    K: 0.043    L: 0.068   
 M: 0.019    N: 0.052    P: 0.057    Q: 0.036    R: 0.044   
 S: 0.066    T: 0.081    V: 0.086    W: 0.003    Y: 0.034   

**********************************************************

Model................................ : JTT
  Number of parameters............... : 597 (0 + 597 branch length estimates)
 -lnL................................ = 63893.71
     (seconds))

Model................................ : LG
  Number of parameters............... : 597 (0 + 597 branch length estimates)
 -lnL................................ = 63452.29
     (seconds))

Model................................ : MtREV
  Number of parameters............... : 597 (0 + 597 branch length estimates)
 -lnL................................ = 68033.93
     (seconds))

Model................................ : Dayhoff
  Number of parameters............... : 597 (0 + 597 branch length estimates)
 -lnL................................ = 64752.10
     (seconds))

Model................................ : WAG
  Number of parameters............... : 597 (0 + 597 branch length estimates)
 -lnL................................ = 63280.69
     (seconds))

Model................................ : CpREV
  Number of parameters............... : 597 (0 + 597 branch length estimates)
 -lnL................................ = 63552.18
     (seconds))

************************************************************
Date   :  Wed Jan 08 05:10:47 IST 2025
Runtime:  0h:02:08



***************************************************************************
Best model according to AICc: WAG
Confidence Interval: 100.0
***************************************************************************
Model          deltaAICc      AICc           AICcw          -lnL           
---------------------------------------------------------------------------
WAG            0.00           125351.30      1.00           63280.69       
LG             343.20         125694.50      0.00           63452.29       
CpREV          542.99         125894.29      0.00           63552.18       
JTT            1226.04        126577.34      0.00           63893.71       
Dayhoff        2942.82        128294.12      0.00           64752.10       
MtREV          9506.48        134857.78      0.00           68033.93       
---------------------------------------------------------------------------
---------------------------------------------------------------------------
***********************************************
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