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PHYLIP - Phylogeny Inference Package (version 3.5)
This is a FREE package of programs for inferring phylogenies and carrying
out certain related tasks. At present it contains 30 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
----------- 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.
The package includes extensive documentation files that provide the information
necessary to use and modify the programs.
Joe Felsenstein
joe@genetics.washington.edu
Department of Genetics
University of Washington
Box 357360
Seattle, Washington 98195-7360, U.S.A.
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