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From: Pav Lucistnik <pav@FreeBSD.org>
Date: Wed, 14 May 2008 13:51:50 +0000 (UTC)
To: ports-committers@FreeBSD.org, cvs-ports@FreeBSD.org, cvs-all@FreeBSD.org
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Cc: 
Subject: cvs commit: ports/biology Makefile ports/biology/muscle Makefile
 distinfo pkg-descr ports/biology/muscle/files patch-Makefile
 patch-globalslinux.cpp patch-intmath.cpp
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pav         2008-05-14 13:51:50 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/muscle       Makefile distinfo pkg-descr 
    biology/muscle/files patch-Makefile patch-globalslinux.cpp 
                         patch-intmath.cpp 
  Log:
  MUSCLE is multiple alignment software for protein and nucleotide sequences.
  The name stands for multiple sequence comparison by log-expectation.
  
  A range of options is provided that give you the choice of optimizing
  accuracy, speed, or some compromise between the two. Default parameters are
  those that give the best average accuracy in the published tests. MUSCLE
  can achieve both better average accuracy and better speed than CLUSTALW or
  T-Coffee, depending on the chosen options.
  
  Citation:
  
  Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
  and high throughput. Nucleic Acids Research 32(5): 1792-1797.
  
  Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
  reduced time and space complexity. BMC Bioinformatics 5(1): 113.
  
  The NAR paper gives only a brief overview of the algorithm and
  implementation details. For a full discussion of the method and many of
  the non-default options that it offers, please see the BMC paper.
  
  WWW: http://www.drive5.com/muscle/
  
  PR:             ports/118460
  Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  
  Revision  Changes    Path
  1.96      +1 -0      ports/biology/Makefile
  1.1       +41 -0     ports/biology/muscle/Makefile (new)
  1.1       +9 -0      ports/biology/muscle/distinfo (new)
  1.1       +35 -0     ports/biology/muscle/files/patch-Makefile (new)
  1.1       +94 -0     ports/biology/muscle/files/patch-globalslinux.cpp (new)
  1.1       +30 -0     ports/biology/muscle/files/patch-intmath.cpp (new)
  1.1       +22 -0     ports/biology/muscle/pkg-descr (new)