PROTPARS

PROTPARS is a Multistate discrete-characters parsimony method. Up to 8 states (as well as "?") are allowed. Cannot do Camin-Sokal or Dollo Parsimony. Can cope with multifurcations, reconstruct ancestral states, use character weights, and infer branch lengths. Part of Phylip.

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

TEST DATA SET

     5    10
Alpha     ABCDEFGHIK
Beta      AB--EFGHIK
Gamma     ?BCDSFG*??
Delta     CIKDEFGHIK
Epsilon   DIKDEFGHIK

CONTENTS OF OUTPUT FILE (with all numerical options on)

 
Protein parsimony algorithm, version 3.6
 
 5 species,  10  sites
 
 
Name          Sequences
----          ---------
 
Alpha        ABCDEFGHIK 
Beta         ..--...... 
Gamma        ?...S..*?? 
Delta        CIK....... 
Epsilon      DIK....... 
 
 
 
 
One most parsimonious tree found:
 
 
 
 
     +--------Gamma     
     !  
  +--2     +--Epsilon   
  !  !  +--4  
  !  +--3  +--Delta     
  1     !  
  !     +-----Beta      
  !  
  +-----------Alpha     
 
  remember: this is an unrooted tree!
 
 
requires a total of     15.000
 
steps in each position:
         0   1   2   3   4   5   6   7   8   9
     *-----------------------------------------
    0!       3   1   4   3   2   0   0   2   0
   10!   0                                    
 
From    To     Any Steps?    State at upper node
                             ( . means same as in the node below it on tree)
 
 
         1                ANCDEFGHIK 
  1      2         no     .......... 
  2   Gamma        yes    ?B..S..*?? 
  2      3         yes    ..?....... 
  3      4         yes    ?IK....... 
  4   Epsilon     maybe   D......... 
  4   Delta        yes    C......... 
  3   Beta         yes    .B--...... 
  1   Alpha       maybe   .B........