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From: Dmitry Marakasov <amdmi3@FreeBSD.org>
Date: Tue, 21 Jul 2009 01:10:13 +0000 (UTC)
To: ports-committers@FreeBSD.org, cvs-ports@FreeBSD.org, cvs-all@FreeBSD.org
X-FreeBSD-CVS-Branch: HEAD
Cc: 
Subject: cvs commit: ports/biology Makefile ports/biology/phyml Makefile
 distinfo pkg-descr ports/biology/phyml/files patch-src-configure
 patch-src-configure.ac
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amdmi3      2009-07-21 01:10:13 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/phyml        Makefile distinfo pkg-descr 
    biology/phyml/files  patch-src-configure 
                         patch-src-configure.ac 
  Log:
  PhyML is a software that estimates maximum likelihood phylogenies from
  alignments of nucleotide or amino acid sequences. It provides a wide range of
  options that were designed to facilitate standard phylogenetic analyses. The
  main strengths of PhyML lies in the large number of substitution models coupled
  to various options to search the space of phylogenetic tree topologies, going
  from very fast and efficient methods to slower but generally more accurate
  approaches. It also implements two methods to evaluate branch supports in a
  sound statistical framework (the non-parametric bootstrap and the approximate
  likelihood ratio test). PhyML was designed to process moderate to large data
  sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
  can analyzed. In practice however, the amount of memory required to process a
  data set is proportional of the product of the number of sequences by their
  length. Hence, a large number of sequences can only be processed provided that
  they are short. Also, PhyML can handle long sequences provided that they are
  not numerous. With most standard personal computers, the "comfort zone" for
  PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
  
  WWW: http://code.google.com/p/phyml/
  
  PR:             136877
  Submitted by:   Ben Allen <ben@sysadminschronicles.com>
  
  Revision  Changes    Path
  1.111     +1 -0      ports/biology/Makefile
  1.1       +31 -0     ports/biology/phyml/Makefile (new)
  1.1       +3 -0      ports/biology/phyml/distinfo (new)
  1.1       +11 -0     ports/biology/phyml/files/patch-src-configure (new)
  1.1       +11 -0     ports/biology/phyml/files/patch-src-configure.ac (new)
  1.1       +18 -0     ports/biology/phyml/pkg-descr (new)