PHYLIP (Phylogeny Inference Package)

Version 3.5c, by Joseph Felsenstein, March 1993



(c) Copyright 1986-1993 by Joseph Felsenstein and the University of Washington. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

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 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.

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

The programs are written in a very standard subset of C, a language that is available on most computers (including microcomputers). The programs require no modifications to run on most machines: for example they work without modification with Microsoft C, Turbo C, Think C, and on the C compilers available on Unix and VAX VMS systems. C source code is distributed in the regular version of PHYLIP. To use it, you must have a C compiler. A Pascal version can also be supplied on request. Executables are available for PCDOS, 386 PCDOS, 386 Windows, and Macintoshes as described below.

NETWORK DISTRIBUTION: The package is available by "anonymous ftp" over electronic networks (including the PCDOS, 386 PCDOS, 386 Windows, and Macintosh executables) from ( Contact me by electronic mail for details or start by fetching file pub/phylip/Read.Me. I can also send the source code and documentation files (but not executables) over Bitnet/EARN and other networks.

DISKETTE DISTRIBUTION: The package is also distributed in a variety of microcomputer diskette formats. You should send FORMATTED diskettes, which I will return with the package written on them. See below for how many diskettes to send. The source code of the programs on the electronic network or magnetic tape versions may of course also be moved to microcomputers and compiled there.

PRECOMPILED VERSIONS: Precompiled executable programs for PCDOS, 386 Windows, 386 PCDOS, and Macintosh systems are available from me. Specify the "386 Windows executable version", "386 PCDOS executable version", "PCDOS executable version" or "Macintosh executable version" and send the number of diskettes indicated below. Source code sent will be in C unless you specify Pascal.

HOW MANY DISKETTES TO SEND: The following table shows for different formats how many diskettes to send, and how many extra diskettes to send for the executable version:

  Diskette size     Density   For source code    For executables send
                              and documentation      in addition
  3.5 inch PCDOS     1.44 Mb         1                     3
  5.25 inch PCDOS    1.2 Mb          1                     3
  3.5 inch PCDOS     720 Kb          2                     4
  5.25 inch PCDOS    360 Kb          8                     5
  Macintosh          800K            2                     3
  Macintosh          High density    1                     1
Some other formats are also available. You MUST tell me EXACTLY which of these formats you need. The diskettes MUST be formatted by you before being sent to me. Sending an extra diskette may be helpful.

TAPE DISTRIBUTION: The programs can also be distributed on an industry-standard 1-inch magnetic tape provided by you. Contact me for details.

POLICIES: The package is distributed free. It will be written on the diskettes or tape, which will be mailed back. They can be sent to:

                                               Joe Felsenstein
Electronic mail addresses:                     Department of Genetics SK-50
 Internet:      University of Washington
 Bitnet/EARN: felsenst@uwavm                   Seattle, Washington 98195, U.S.A.

Maintained 15 Jul 1996 -- by Martin Hilbers(

Lee Kozar / Manager, Bioinformatics Resource /