DNAPARS 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 AACGUGGCCAAAU Beta AAGGUCGCCAAAC Gamma CAUUUCGUCACAA Delta GGUAUUUCGGCCU Epsilon GGGAUCUCGGCCC |
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 |