joe@GENETICS.WASHINGTON.EDU (Joe Felsenstein) (06/15/91)
PHYLIP 3.4 RELEASED
Version 3.4 of PHYLIP, a free package of programs for inferring phylogenies
from various kinds of data, was released on 14 June. Generic source code in
Pascal, documentation, and PCDOS executables are available for free from me
as usual on diskette, by anonymous ftp from evolution.genetics.washington.edu,
by e-mail, or on tape. Below I have appended the PHYLIP general information
notice which describes details of distribution.
There are many changes from the previous version. Here is a summary of
the major changes since version 3.3:
1. All programs now have interactive menus for the user to choose options
and details of the analysis. All write results to output files and
trees to tree files by default. It is no longer necessary to modify the
input files to specify most options.
2. Three new programs have been added: SEQBOOT is a general bootstrapping
tool allowing sequences, restriction sites patterns, morphological data,
etc. to be bootstrapped. NEIGHBOR performs the Neighbor-Joining
and UPGMA distance matrix methods, and can handle much larger cases than
the other distance methods owing to its higher speed. CONTRAST reads in
a tree and a data set and computes the contrasts between species that are
needed in comparative methods.
3. Almost all programs have been changed to read in multiple data sets, so
together with SEQBOOT and the consensus tree program CONSENSE this allows
most kinds of analysis in the package to be bootstrapped.
4. All sequence methods now allow input data to be in either "interleaved"
or "sequential" format (i.e. the PHYLIP 3.3 format or the earlier one).
5. There have been corrections and improvements in the tree-drawing programs,
which can now produce output for an HP Laserjet, for PC Paintbrush .PCX
format files, and for Macintosh screens.
6. SEQBOOT also allows the J.Archie/D.Faith method of permutation of species
within characters to test for the absence of significant evidence of
phylogenetic structure,
7. The DNA Maximum Likelihood program DNAML is now about 60% faster.
8. The restriction site maximum likelihood program RESTML now allows for the
fact that the data may have been generated by use of multiple enzymes.
The programs will be found in directory "pub" in the ftp area of my
computer "evolution.genetics.washington.edu" (IP number 128.95.12.41)
in the form of two compressed tar archives (one for sources and documents
and one for PCDOS executables), and also as Zoo archives which will
self-extract on PCDOS machines. We hope to have self-extracting Macintosh
archives of sources and Mac executables available for ftp by 19 June 1991.
I will shortly post a notice listing phylogeny packages currently available
that I know about. Here is the PHYLIP information sheet with further
details of distribution.
-----
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
Internet: joe@genetics.washington.edu (IP No. 128.95.12.41)
Bitnet/EARN: felsenst@uwavm
UUCP: ... uw-beaver!evolution.genetics!joe
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PHYLIP - Phylogeny Inference Package (version 3.4)
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
DNABOOT Bootstraps DNA parsimony DNACOMP Compatibility for DNA
DNAINVAR Phylogenetic invariants DNAML Maximum likelihood method
DNAMLK DNAML with molecular clock DNADIST Distances from sequences
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 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 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
The package includes extensive documentation files that 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
modifications on VAX VMS Pascal. Pascal source code is distributed in the
regular version of PHYLIP: compiled object code is not. To use that version,
you must have a Pascal compiler.
DISKETTE DISTRIBUTION: The package is 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 systems are
available from me. Specify the "PCDOS executable version" and send the number
of extra diskettes indicated below. An Apple Macintosh version with
precompiled code is available from me or from Willem Ellis, Instituut voor
Taxonomische Zoologie, Zoologisch Museum, Universiteit van Amsterdam, Plantage
Middenlaan 64, 1018DH Amsterdam, Netherlands, if you send either of us 5 800K
diskettes.
HOW MANY DISKETTES TO SEND: The following table shows for different PCDODS
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 send in addition
3.5 inch 1.44 Mb 2 2
5.25 inch 1.2 Mb 3 2
3.5 inch 720 Kb 4 3
5.25 inch 360 Kb 8 5
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.
NETWORK DISTRIBUTION: The package is also available by distribution of the
files directly over electronic networks, and by anonymous ftp (including PCDOS
and Macintosh executables) from evolution.genetics.washington.edu. Contact me
by electronic mail for details or start by fetching file pub/phylip.read.me.
TAPE DISTRIBUTION: The programs can also be distributed on a magnetic tape
provided by you (which should be a small tape and need only be able to hold two
megabytes). Contact me for details.
POLICIES: The package is distributed free. I do not make it available or
support it in South Africa. The package 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: joe@genetics.washington.edu University of Washington
Bitnet/EARN: felsenst@uwavm Seattle, Washington 98195
UUCP: ... uw-beaver!evolution.genetics!joe U.S.A.