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46 lines
2.6 KiB
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46 lines
2.6 KiB
Plaintext
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PHYLIP - Phylogeny Inference Package (version 3.5)
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This is a FREE package of programs for inferring phylogenies and carrying
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out certain related tasks. At present it contains 30 programs, which carry out
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different algorithms on different kinds of data. The programs in the package
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are:
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---------- Programs for molecular sequence data ----------
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PROTPARS Protein parsimony DNAPARS Parsimony method for DNA
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DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA
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DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants
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DNAML Maximum likelihood method DNAMLK DNA ML with molecular clock
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DNADIST Distances from sequences PROTDIST Distances from proteins
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RESTML ML for restriction sites SEQBOOT Bootstraps sequence data sets
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----------- Programs for distance matrix data ------------
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FITCH Fitch-Margoliash and least-squares methods
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KITSCH Fitch-Margoliash and least squares methods with evolutionary clock
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NEIGHBOR Neighbor-joining and UPGMA methods
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-------- Programs for gene frequencies and continuous characters -------
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CONTML Maximum likelihood method GENDIST Computes genetic distances
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CONTRAST Computes contrasts and correlations for comparative method studies
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------------- Programs for 0-1 discrete state data -----------
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MIX Wagner, Camin-Sokal, and mixed parsimony criteria
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MOVE Interactive Wagner, C-S, mixed parsimony program
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PENNY Finds all most parsimonious trees by branch-and-bound
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DOLLOP, DOLMOVE, DOLPENNY same as preceding four programs, but for
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the Dollo and polymorphism parsimony criteria
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CLIQUE Compatibility method FACTOR recode multistate characters
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---------- Programs for plotting trees and consensus trees -------
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DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers
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DRAWTREE Draws unrooted phylogenies on screens, plotters and printers
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CONSENSE Majority-rule and strict consensus trees
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RETREE Reroots, changes names and branch lengths, and flips trees
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There is also an Unsupported Division containing two programs, makeinf and
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ProtML, which were contributed by others and are maintained by their authors.
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The package includes extensive documentation files that provide the information
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necessary to use and modify the programs.
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Joe Felsenstein
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joe@genetics.washington.edu
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Department of Genetics
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University of Washington
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Box 357360
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Seattle, Washington 98195-7360, U.S.A.
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