This is a package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 31 programs, which carry out different algorithms on different kinds of data. The programs in the package are:
Programs for molecular sequence data
PROTPARS Protein parsimony DNAPARS Parsimony method for DNA DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants DNAML Maximum likelihood method DNAMLK DNA ML with molecular clock DNADIST Distances from sequences PROTDIST Distances from proteins RESTML ML for restriction sites SEQBOOT Bootstraps sequence data sets COALLIKE Coalescent likelihoods from sampled phylogeny estimates
Programs for distance matrix data
FITCH Fitch-Margoliash and least-squares methods KITSCH Fitch-Margoliash and least squares methods with evolutionary clock NEIGHBOR Neighbor-joining and UPGMA methods
Programs for gene frequencies and continuous characters
CONTML Maximum likelihood method GENDIST Computes genetic distances CONTRAST Computes contrasts and correlations for comparative method studies
Programs for 0-1 discrete state data
MIX Wagner, Camin-Sokal, and mixed parsimony criteria
MOVE Interactive Wagner, C-S, mixed parsimony program
PENNY Finds all most parsimonious trees by branch-and-bound
DOLLOP, DOLMOVE, DOLPENNY same as preceding four programs, but for
the Dollo and polymorphism parsimony criteria
CLIQUE Compatibility method FACTOR recode multistate characters
Programs for plotting trees and consensus trees
DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers DRAWTREE Draws unrooted phylogenies on screens, plotters and printers CONSENSE Majority-rule and strict consensus trees RETREE Reroots, changes names and branch lengths, and flips trees
There is also an Unsupported Division containing two programs, makeinf and ProtML, which were contributed by others and are maintained by their authors.
Short Descriptions of all PHYLIP programs
An Overview of the Input and Output formats
Programs that directly analyze DNA or Protein sequences
Frequently Asked Questions about PHYLIP
The Complete PHYLIP Documentation