PHYLIP 3.4 RELEASED

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Fri Jun 14 19:17:41 EST 1991


                            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 at genetics.washington.edu     (IP No. 128.95.12.41)
 Bitnet/EARN:      felsenst at uwavm
 UUCP:             ... uw-beaver!evolution.genetics!joe

---------------------------------------------------------------------------  

              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 at genetics.washington.edu          University of Washington
 Bitnet/EARN: felsenst at uwavm                       Seattle, Washington 98195
 UUCP:    ... uw-beaver!evolution.genetics!joe     U.S.A.




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