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 treesThere 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 evolution.genetics.washington.edu (188.8.131.52). 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 1Some 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: email@example.com University of Washington Bitnet/EARN: felsenst@uwavm Seattle, Washington 98195, U.S.A.
Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)
Lee Kozar / Manager, Bioinformatics Resource / firstname.lastname@example.org