ports/118460: commit references a PR

[dfilter service]

The following reply was made to PR ports/118460; it has been noted by GNATS.

From: dfilter at FreeBSD.ORG (dfilter service)
To: bug-followup at FreeBSD.org
Cc:  
Subject: Re: ports/118460: commit references a PR
Date: Wed, 14 May 2008 13:52:07 +0000 (UTC)

 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 at 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)
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