v3.6

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
protparsprotein parsimony documentation file
dnaparsDNA sequence parsimony documentation file
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 file
protdistProtein sequence distance documentation file
restdistRestriction sites and fragments distances documentation file
restmlRestriction sites maximum likelihood documentation file
seqbootBootstrapping/Jackknifing documentation file

Distance matrix methods

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

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

Tree drawing, consensus, tree editing, tree distances

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