FITCH
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 = DNA distance matrix
TEST DATA SET
7 Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083 Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000
OUTPUT FROM TEST DATA SET (with all numerical options on)
7 Populations Fitch-Margoliash method version 3.66
__ __ 2 \ \ (Obs - Exp) Sum of squares = /_ /_ ------------ 2 i j Obs Negative branch lengths not allowed Name Distances ---- -------- Bovine 0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050 Mouse 1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290 Gibbon 1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830 Orang 1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100 Gorilla 1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830 Chimp 1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920 Human 1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000 +---------------------------------------------Mouse !
! +------Human
! +--5
! +-4 +--------Chimp
! ! !
! +--3 +---------Gorilla
! ! !
1------------------------2 +-----------------Orang
! !
! +---------------------Gibbon
!
+------------------------------------------------------Bovine remember: this is an unrooted tree! Sum of squares = 0.01375 Average percent standard deviation = 1.85418 Between And Length ------- --- ----- 1 Mouse 0.76985
1 2 0.41983
2 3 0.04986
3 4 0.02121
4 5 0.03695
5 Human 0.11449
5 Chimp 0.15471
4 Gorilla 0.15680
3 Orang 0.29209
2 Gibbon 0.35537
1 Bovine 0.91675