gribskov@FCRFV1.NCIFCRF.GOV (Gribskov, Michael) (02/13/90)
My understanding is that PHYLIP is available at no charge from it's author, Joseph Felsenstein. I have the following addresses: Felsenstein, Joseph - FELSENST@UWALOCKE Felsenstein, Joseph - uw-beaver!uw-entropy!uw-evolution!joe (UUCP) Felsenstein, Joseph * joe@genetics.washington.edu (ARPA) I think the last one is preferred. If someone finds out details, I suggest that they post it to infogcg. Michael Gribskov GRIBSKOV@NCIFCRF.GOV
clark@MSHRI.UTORONTO.CA (02/14/90)
/My understanding is that PHYLIP is available at no charge from it's /author, Joseph Felsenstein. I have the following addresses: What's PHYLIP? Steve Clark clark@mshri.utoronto.ca (Internet) sinai@utoroci (Netnorth/Bitnet)
GOLUB@PENNDRLS.BITNET (Ellis Golub) (02/14/90)
The following information was forwarded to me from Joe Felsenstein:
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From: Joe Felsenstein <joe@genetics.washington.edu>
Message-Id: <9002081831.AA28149@evolution.genetics.washington.edu>
Subject: Re: PHYLIP
To: GOLUB%PENNDRLS.BITNET@uwavm.acs.washington.edu (Ellis Golub)
Date: Thu, 8 Feb 90 10:31:55 PDT
In-Reply-To: <E03B8DBA1DDF00036E@locke.hs.washington.edu>; from
"GOLUB@PENNDRLS.BITNET" at Feb 8, 90 0916
X-Mailer: ELM [version 2.2 PL0]
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. 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. See below for how many diskettes to send. The programs on the
magnetic tape or electronic mail versions 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 the number of extra diskettes indicated
below. 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.
HOW MANY DISKETTES TO SEND: The following table shows for different PCDOS
formats how many diskettes to send, and how many extra diskettes to send
for the PCDOS executable version:
Diskette size Density For source code: For executables also send:
3.5 inch 1.44 Mb 2 1
5.25 inch 1.2 Mb 2 1
3.5 inch 720 Kb 4 2
5.25 inch 360 Kb 7 4
Some other formats including CP/M-80 Kaypro II are 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.
NETWORK DISTRIBUTION: The package is also available by distribution of the
source code and documentation files directly by electronic mail. Keep in mind
that this involves sending 72 files and 2.2 Megabytes. Contact me by
electronic mail to request this. The package is also available by anonymous
ftp.
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 one describes the contents of the
package.
POLICIES: The package is distributed free. I do not make it available or
support it in South Africa. The package will be sent by electronic mail
or 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.
Internet/ARPANet: joe@genetics.washington.edu
BITNET/EARNET: FELSENST@UWALOCKE
UUCP: ... uw-beaver!evolution.genetics!joe
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From the ashes of:
Ellis Golub
Biochemistry Department
University of Pennsylvania
School of Dental Medicine
4001 Spruce Street
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Phone: (215) 898-4629
FAX: (215) 898-3695
GOLUB @ PENNDRLS (Bitnet)