
----------------------------------------------------------------------------------------------
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:     Sun May 17 17:05:45 UTC 2026
OS:       Linux (6.6.122+)
Arch:     amd64
Java:     17.0.18 (Ubuntu)
PhyML:    /content/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.................: 399.0
  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: 35
Observed aminoacid frequencies:
 A: 0.100    C: 0.015    D: 0.044    E: 0.030    F: 0.057   
 G: 0.076    H: 0.005    I: 0.045    K: 0.034    L: 0.059   
 M: 0.019    N: 0.055    P: 0.080    Q: 0.042    R: 0.053   
 S: 0.080    T: 0.086    V: 0.077    W: 0.011    Y: 0.031   

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

Model................................ : JTT
  Number of parameters............... : 37 (0 + 37 branch length estimates)
 -lnL................................ = 8992.36
     (seconds))

Model................................ : LG
  Number of parameters............... : 37 (0 + 37 branch length estimates)
 -lnL................................ = 8926.32
     (seconds))

Model................................ : MtREV
  Number of parameters............... : 37 (0 + 37 branch length estimates)
 -lnL................................ = 9504.19
     (seconds))

Model................................ : Dayhoff
  Number of parameters............... : 37 (0 + 37 branch length estimates)
 -lnL................................ = 9008.85
     (seconds))

Model................................ : WAG
  Number of parameters............... : 37 (0 + 37 branch length estimates)
 -lnL................................ = 8922.49
     (seconds))

Model................................ : CpREV
  Number of parameters............... : 37 (0 + 37 branch length estimates)
 -lnL................................ = 9050.46
     (seconds))

************************************************************
Date   :  Sun May 17 17:05:51 UTC 2026
Runtime:  0h:00:06



***************************************************************************
Best model according to AICc: WAG
Confidence Interval: 100.0
***************************************************************************
Model          deltaAICc      AICc           AICcw          -lnL           
---------------------------------------------------------------------------
WAG            0.00           17926.77       0.98           8922.49        
LG             7.66           17934.43       0.02           8926.32        
JTT            139.74         18066.51       0.00           8992.36        
Dayhoff        172.73         18099.50       0.00           9008.85        
CpREV          255.94         18182.71       0.00           9050.46        
MtREV          1163.39        19090.16       0.00           9504.19        
---------------------------------------------------------------------------
---------------------------------------------------------------------------
***********************************************
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
