PARS

PARS estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished. Part of Phylip.

Manual: http://evolution.genetics.washington.edu/phylip/doc/pars.html

TEST DATA SET

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

TEST SET OUTPUT (with all numerical options on)

 
Discrete character parsimony algorithm, version 3.6
 
 5 species,   6  sites
 
 
Name         Sequences
----         ---------
 
Alpha        110110
Beta         ...00.
Gamma        .0....
Delta        001001
Epsilon      001...
 
 
 
One most parsimonious tree found:
 
 
                            +Epsilon   
           +----------------3  
  +--------2                +-------------------------Delta     
  |        |  
  |        +Gamma     
  |  
  1----------------Beta      
  |  
  +Alpha     
 
 
requires a total of      8.000
 
  between      and       length
  -------      ---       ------
     1           2         1.00
     2           3         2.00
     3      Epsilon        0.00
     3      Delta          3.00
     2      Gamma          0.00
     1      Beta           2.00
     1      Alpha          0.00
 
steps in each site:
         0   1   2   3   4   5   6   7   8   9
     *-----------------------------------------
    0|       1   1   1   2   2   1            
 
From    To     Any Steps?    State at upper node
                             ( . means same as in the node below it on tree)
 
          1                110110
   1      2         yes    .0....
   2      3         yes    0.1...
   3   Epsilon      no     ......
   3   Delta        yes    ...001
   2   Gamma        no     ......
   1   Beta         yes    ...00.
   1   Alpha        no     ......