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1.4
date	2009.12.21.02.15.54;	author dougb;	state Exp;
branches;
next	1.3;

1.3
date	2001.08.22.10.02.27;	author wjv;	state Exp;
branches;
next	1.2;

1.2
date	2001.04.02.05.10.14;	author mharo;	state Exp;
branches;
next	1.1;

1.1
date	2000.07.10.03.25.48;	author steve;	state Exp;
branches;
next	;


desc
@@


1.4
log
@For ports maintained by ports@@FreeBSD.org, remove names and/or
e-mail addresses from the pkg-descr file that could reasonably
be mistaken for maintainer contact information in order to avoid
confusion on the part of users looking for support. As a pleasant
side effect this also avoids confusion and/or frustration for people
who are no longer maintaining those ports.
@
text
@              PHYLIP - Phylogeny Inference Package (version 3.6)

PHYLIP (the PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees).  Methods that are
available in the package include parsimony, distance matrix, and
likelihood methods, including bootstrapping and consensus trees. Data
types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.

 Joe Felsenstein
 Department of Genetics
 University of Washington
 Box 357360
 Seattle, Washington 98195-7360, U.S.A.

WWW: http://evolution.genetics.washington.edu/phylip.html
@


1.3
log
@- Update to version 3.6.a2.1 - since the distribution tarball hadn't been
  renamed between versions, this port failed checksum.
- Apply some whitespace edits and cut pkg-descr down to size to placate
  portlint.

Reported by:	Jason Stajich <jason@@chg.mc.duke.edu>
Approved by:	No response from MAINTAINER
@
text
@a11 1
 joe@@genetics.washington.edu
@


1.2
log
@updated port biology/phylip from vers 3.5 to 3.6

PR:		26146
Submitted by:	    "David A. Bader" <dbader@@eece.unm.edu>
@
text
@a10 22
The programs are controlled through a menu, which asks the users which
options they want to set, and allows them to start the
computation. The data are read into the program from a text file,
which the user can prepare using any word processor or text editor
(but it is important that this text file not be in the special format
of that word processor -- it should instead be in "flat ASCII" or
"Text Only" format). Some sequence analysis programs such as alignment
programs can write data files in the PHYLIP format. Most of the
programs look for the data in a file called "infile" -- if they do not
find this file they then ask the user to type in the file name of the
data file.

Output is written onto special files with names like "outfile" and
"treefile". Trees written onto "treefile" are in the Newick format, an
informal standard agreed to in 1986 by authors of a number of major
phylogeny packages.

PHYLIP is the most widely-distributed phylogeny package, and competes
with PAUP to be the one responsible for the largest number of
published trees. PHYLIP has been in distribution since 1980, and has
over 6,000 registered users.

d18 1
a18 1
WWW: http://evolution.genetics.washington.edu/phylip.html@


1.1
log
@Adding phylip version 3.5.

This is a FREE package of programs for inferring phylogenies and carrying
out certain related tasks.  At present it contains 30 programs, which carry
out different algorithms on different kinds of data.

PR:		19705
Submitted by:	David A. Bader <dbader@@cielo.eece.unm.edu>
@
text
@d1 1
a1 1
              PHYLIP - Phylogeny Inference Package (version 3.5)
d3 38
a40 43
     This is a FREE package of programs for inferring phylogenies and  carrying
out certain related tasks.  At present it contains 30 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
      ----------- 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 trees

There 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.

                             Joe Felsenstein
                             joe@@genetics.washington.edu
                             Department of Genetics
                             University of Washington
                             Box 357360
                             Seattle, Washington 98195-7360, U.S.A.
@

