DNADIST 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.
INPUT = aligned dna sequence files
5 13 Alpha AACGTGGCCACAT Beta AAGGTCGCCACAC Gamma CAGTTCGCCACAA Delta GAGATTTCCGCCT Epsilon GAGATCTCCGCCC |
(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 |