Bug 118460 - New port: biology/muscle multiple alignment software
Summary: New port: biology/muscle multiple alignment software
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: freebsd-ports-bugs (Nobody)
Depends on:
Reported: 2007-12-06 12:40 UTC by Motomichi Matsuzaki
Modified: 2008-05-14 15:00 UTC (History)
0 users

See Also:

file.shar (7.38 KB, text/plain)
2007-12-06 12:40 UTC, Motomichi Matsuzaki
no flags Details

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Description Motomichi Matsuzaki 2007-12-06 12:40:01 UTC
MUSCLE is a multiple alignment software for protein and nucleotide sequences,
and can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee.

Fix: Patch attached with submission follows:
Comment 1 Pav Lucistnik freebsd_committer 2008-05-14 14:42:02 UTC
State Changed
From-To: open->closed

New port added, thanks!
Comment 2 dfilter service freebsd_committer 2008-05-14 14:52:07 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 
  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.
  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)
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