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.