PHYLIP

This is a free 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.

PHYLIP was written by Joseph Felsenstein at the University of Washington.

The package includes extensive documentation files that provide the information necessary to use and modify the programs.

Installed on the Opteron Cluster.

Program documentation:

• An overview of the programs FITCH, KITSCH, and NEIGHBOR, which deal with data in the form of a matrix of pairwise distances between all pairs of taxa.
• An overview of the interactive tree plotting programs DRAWTREE and DRAWGRAM .
• The main PHYLIP documentation.
• The individual programs in the package are:

  Programs for molecular sequence data

  • PROTPARS Protein parsimony
  • DNAPARS Parsimony method for DNA
  • DNAMOVE Interactive DNA parsimony
  • 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

  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

See also:

• The PHYLIP web site at the University of Washington.
• Other phylogeny software installed at the PSC.