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.
© Copyright 1991-2006 by the University of Washington. Written by Joseph Felsenstein. Edited by NGBW team.
Manual: http://evolution.genetics.washington.edu/phylip/doc/pars.html
INPUT: Discrete Character Matrix
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 ......