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.
© Copyright 1991-2006 by the University of Washington. Written by Joseph Felsenstein. Edited by NGBW team.
Manual: http://evolution.genetics.washington.edu/phylip/doc/protpars.html
INPUT: Aligned Protein Sequences (Character Matrix)
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 15.00
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........