v3.6

PHYLIP programs and documentation

PHYLIP, the PHYLogeny Inference Package, consists of 34 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
protparsprotein parsimony documentation filego
dnaparsDNA sequence parsimony documentation filego
dnapennyDNA parsimony branch and bound documentation file
dnamoveinteractive DNA parsimony documentation file
dnacompDNA compatibility documentation file
dnamlDNA maximum likelihood documentation file
dnamlkDNA maximum likelihood with clock documentation file
promlProtein sequence maximum likelihood documentation file
promlkProtein sequence maximum likelihood with clock documentation file
dnainvarDNA invariants documentation file
dnadistDNA distance documentation filego
protdistProtein sequence distance documentation filego
restdistRestriction sites and fragments distances documentation file
seqbootBootstrapping/Jackknifing documentation filego

Distance matrix methods

Distance matrix programs documentation file
fitchFitch-Margoliash distance matrix method documentation filego
kitschFitch-Margoliash distance matrix with clock documentation filego
neighborNeighbor-Joining and UPGMA method documentation filego

Gene frequencies and continuous characters

Continuous characters and gene frequencies documentation file
contmlMaximum likelihood continuous characters and gene frequencies documentation file
contrastContrast method documentation file
gendistGenetic distance documentation file

Discrete characters methods

Discrete characters methods documentation file
parsUnordered multistate parsimony documentation filego
mixMixed method parsimony documentation filego
pennyBranch and bound mixed method parsimony documentation file
moveInteractive mixed method parsimony documentation file
dollopDollo and polymorphism parsimony documentation filego
dolpennyDollo and polymorphism branch and bound parsimony documentation file
dolmoveDollo and polymorphism interactive parsimony documentation file
clique0/1 characters compatibility method documentation filego
factorCharacter recoding program documentation file

Tree drawing, consensus, tree editing, tree distances

Tree drawing programs documentation file
drawgramRooted tree drawing program documentation filego
drawtreeUnrooted tree drawing program documentation filego
fastDNAmlTree drawing program documentation file go
consenseConsensus tree program documentation filego
treedistTree distance program documentation file
retreeinteractive tree rearrangement program documentation file