dbd%benden@LANL.GOV (Dan Davison) (07/26/89)
===================== PHYLIP Information Notice ============================
PHYLIP - Phylogeny Inference Package (version 3.2)
This is a FREE package of programs for inferring phylogenies and carrying out
certain related tasks. At present it contains 29 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
DNABOOT Bootstraps DNA parsimony DNACOMP Compatibility for DNA
DNAINVAR Phylogenetic invariants DNAML Maximum Likelihood method
DNADIST Makes distance matrix RESTML ML for restriction sites data
----------- Programs for distance matrix data ------------
FITCH Fitch-Margoliash and least-squares methods
KITSCH F-M and L-S methods with evolutionary clock
------- Programs for gene frequencies and continuous characters -------
CONTML Maximum likelihood method GENDIST Computes genetic distances
----------- Programs for 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
BOOT Bootstrap confidence interval on mixed parsimony methods
DOLLOP, DOLMOVE, DOLPENNY, DOLBOOT same as the preceding four
programs, but for the Dollo and polymorphism parsimony criteria
CLIQUE Compatibility method FACTOR recodes multistate characters
---------- Programs for plotting trees and consensus trees --------
PLOTREE, DOTREE Draw phylogenies on pen plotters, dot-matrix printers
PLOTGRAM, DOTGRAM Draw cladograms and phenograms
CONSENSE Majority-rule and strict consensus trees
The package includes extensive documentation files which provide the
information necessary to use and modify the programs.
COMPATIBILITY: The programs are written in a very standard subset of Pascal,
a language that is available on most computers (including microcomputers). The
programs require only trivial modifications to run on most machines. For
example, they work with only minor modifications with Turbo Pascal, and without
modification on VAX VMS Pascal. The Pascal source code is distributed; in the
regular version of PHYLIP compiled executable code is not. To use this version
you must have access to a Pascal compiler.
DISKETTE FORMATS: The package is distributed on a variety of microcomputer
diskette formats. You should send formatted diskettes, which I will return
with the package written on them. Unfortunately, I cannot write any Apple
formats. The 5-inch formats available include IBM PC/AT 1.2 Mb format, IBM
PCDOS (MSDOS) 360K double-sided format and a number of CP/M-80 formats
including Kaypro II. The 3.5-inch double-sided 720K format is 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. Send 2 diskettes for PC/AT 1.2 Mb
format, 7 for the double-sided double-density PCDOS format, and 4 for the
double-sided 3.5-inch formats. For other formats you need enough diskettes to
hold 2.2 megabytes. Sending an extra diskette may be helpful. The programs on
the magnetic tape version may of course also be moved to microcomputers using a
terminal program.
PRECOMPILED VERSIONS: Precompiled executable programs for PCDOS systems,
produced by George D.F. Wilson, are available from me. Specify the "PCDOS
executable version" and send extra diskettes (one more if 5-inch PC/AT 1.2Mb
format, 4 more if 5-inch PCDOS 360K format, and 2 more if 3-inch 720K format).
An Apple Macintosh version with pre-compiled code is available from Willem
Ellis, Instituut voor Taxonomische Zoologie, Zoologisch Museum, Universiteit
van Amsterdam, Plantage Middenlaan 64, 1018 DH Amsterdam, Netherlands, who
should be contacted for details. An Atari ST version is also available.
TAPE DISTRIBUTION: The programs are also distributed on a magnetic tape
provided by you (which should be a small tape and need only be able to hold
two megabytes) in the following format: 9-track, ASCII, odd parity,
unlabelled, 6250 bpi (unless otherwise indicated). Logical record: 80-column
card image (80 bytes), physical record: 3200 bytes (i.e. blocking factor 40).
There are a total of 72 files. The first describes the contents of the
package.
NETWORK DISTRIBUTION: The package is also available by distribution of the
files directly over BITNET. Keep in mind that this involves sending 72 files
and 2.2 Megabytes.
POLICIES: The package is distributed free. I do not make it available or
support it in South Africa or Namibia. The package will be written on
the diskettes or tape, which will be mailed back. They can be sent to:
Joe Felsenstein
Department of Genetics SK-50
University of Washington
Electronic mail addresses: Seattle, Washington 98195, U.S.A.
BITNET/EARN: FELSENST@UWALOCKE
INTERNET/Arpanet: joe%uw-evolution.UUCP@entropy.ms.washington.edu
UUCP: ... uw-beaver!uw-entropy!uw-evolution!joe
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