Date: Wed, 14 May 2008 14:00:03 GMT From: dfilter@FreeBSD.ORG (dfilter service) To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/118460: commit references a PR Message-ID: <200805141400.m4EE03Ke077409@freefall.freebsd.org>
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The following reply was made to PR ports/118460; it has been noted by GNATS.
From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@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@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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