DNADIST
DNADIST. 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.when it is not known in advance which ones are which. 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/dnadist.html
INPUT = aligned DNA sequence files
DNADIST TEST DATA SET
5 13
Alpha AACGTGGCCACAT
Beta AAGGTCGCCACAC
Gamma CAGTTCGCCACAA
Delta GAGATTTCCGCCT
Epsilon GAGATCTCCGCCC
CONTENTS OF OUTPUT FILE (with all numerical options on)
(Note that when the options for displaying the input data are turned off, the output is in a form suitable for use as an input file in the distance matrix programs).
Nucleic acid sequence Distance Matrix program, version 3.6
5 species, 13 sites
F84 Distance
Transition/transversion ratio = 2.000000
Name Sequences
---- ---------
Alpha AACGTGGCCA CAT
Beta ..G..C.... ..C
Gamma C.GT.C.... ..A
Delta G.GA.TT..G .C.
Epsilon G.GA.CT..G .CC
Empirical Base Frequencies:
A 0.24615
C 0.36923
G 0.21538
T(U) 0.16923
Alpha 0.000000 0.303893 0.857546 1.158921 1.542897
Beta 0.303893 0.000000 0.339731 0.913519 0.619666
Gamma 0.857546 0.339731 0.000000 1.631729 1.293707
Delta 1.158921 0.913519 1.631729 0.000000 0.165882
Epsilon 1.542897 0.619666 1.293707 0.165882 0.000000