DNAPARS
DNAPARS. This program uses nucleotide sequences to compute a distance matrix, under three different models of nucleotide substitution. The distance for each pair of species estimates the total branch length between the two species, and can be used in the distance matrix programs FITCH, KITSCH or NEIGHBOR. This is an alternative to use of the sequence data itself in the maximum likelihood program DNAML or the parsimony program DNAPARS. 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/dnapars.html
INPUT = aligned DNA sequence files
TEST DATA SET
5 13Alpha AACGUGGCCAAAU
Beta AAGGUCGCCAAAC
Gamma CAUUUCGUCACAA
Delta GGUAUUUCGGCCU
Epsilon GGGAUCUCGGCCC
CONTENTS OF OUTPUT FILE (if all numerical options are on)
DNA parsimony algorithm, version 3.6
5 species, 13 sites
Name Sequences
---- ---------
Alpha AACGUGGCCA AAU
Beta ..G..C.... ..C
Gamma C.UU.C.U.. C.A
Delta GGUA.UU.GG CC.
Epsilon GGGA.CU.GG CCC
One most parsimonious tree found:
+-----Epsilon
+----------------------------3
+------------2 +-------Delta
| |
| +----------------Gamma
|
1----Beta
|
+---------Alpha
requires a total of 19.000
between and length
------- --- ------
1 2 0.217949
2 3 0.487179
3 Epsilon 0.096154
3 Delta 0.134615
2 Gamma 0.275641
1 Beta 0.076923
1 Alpha 0.173077
steps in each site:
0 1 2 3 4 5 6 7 8 9
*-----------------------------------------
0| 2 1 3 2 0 2 1 1 1
10| 1 1 1 3
From To Any Steps? State at upper node
( . means same as in the node below it on tree)
1 AABGTCGCCA AAY
1 2 yes V.KD...... C..
2 3 yes GG.A..T.GG .C.
3 Epsilon maybe ..G....... ..C
3 Delta yes ..T..T.... ..T
2 Gamma yes C.TT...T.. ..A
1 Beta maybe ..G....... ..C
1 Alpha yes ..C..G.... ..T