PHYLIP programs and documentation

PHYLIP, the PHYLogeny Inference Package, consists of 35 programs. There are documentation files for each program, in the form of web pages in HTML 3.2. There are also documentation web pages for each group of programs, and a main documentation file that is the basic introduction to the package. Before running any of the programs you should read it.
Below you will find a list of the programs and the documentation files. The names of the documentation files are highlighted as links that will take you to those documentation files.

Introduction to PHYLIP
main documentation file

Molecular sequence methods
molecular sequence programs documentation file
protpars
protein parsimony documentation file
dnapars
DNA sequence parsimony documentation file
dnapenny
DNA parsimony branch and bound documentation file
dnamove
interactive DNA parsimony documentation file
dnacomp
DNA compatibility documentation file
dnaml
DNA maximum likelihood documentation file
dnamlk
DNA maximum likelihood with clock documentation file
proml
Protein sequence maximum likelihood documentation file
promlk
Protein sequence maximum likelihood with clock documentation file
dnainvar
DNA invariants documentation file
dnadist
DNA distance documentation file
protdist
Protein sequence distance documentation file
restdist
Restriction sites and fragments distances documentation file
restml
Restriction sites maximum likelihood documentation file
seqboot
Bootstrapping/Jackknifing documentation file

Distance matrix methods
Distance matrix programs documentation file
fitch
Fitch-Margoliash distance matrix method documentation file
kitsch
Fitch-Margoliash distance matrix with clock documentation file
neighbor
Neighbor-Joining and UPGMA method documentation file

Gene frequencies and continuous characters
Continuous characters and gene frequencies documentation file
contml
Maximum likelihood continuous characters and gene frequencies documentation file
contrast
Contrast method documentation file
gendist
Genetic distance documentation file
Discrete characters methods
Discrete characters methods documentation file
pars
Unordered multistate parsimony documentation file
mix
Mixed method parsimony documentation file
penny
Branch and bound mixed method parsimony documentation file
move
Interactive mixed method parsimony documentation file
dollop
Dollo and polymorphism parsimony documentation file
dolpenny
Dollo and polymorphism branch and bound parsimony documentation file
dolmove
Dollo and polymorphism interactive parsimony documentation file
clique
0/1 characters compatibility method documentation file
factor
Character recoding program documentation file
Tree drawing, consensus, tree editing, tree distances
Tree drawing programs documentation file
drawgram
Rooted tree drawing program documentation file
drawtree
Unrooted tree drawing program documentation file


consense
Consensus tree program documentation file
treedist
Tree distance program documentation file
retree
interactive tree rearrangement program documentation file