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Port details
muscle MUltiple Sequence Comparison by Log-Expectation
3.8.31 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 14 May 2008 13:52:50
License: not specified in port
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/
SVNWeb : Homepage : Distfiles Availability : PortsMonThere are no ports dependent upon this port

To install the port: cd /usr/ports/biology/muscle/ && make install clean
To add the package: pkg install biology/muscle


Configuration Options
     No options to configure

USES:
dos2unix

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/
  2. http://www.drive5.com/muscle/downloads3.8.31/

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
17 Jun 2014 21:36:06
Original commit files touched by this commit  3.8.31
Revision:358182
rakuco search for other commits by this committer
Update to 3.8.31.

PR:		191130
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
01 Jun 2014 11:05:44
Original commit files touched by this commit  3.6
Revision:356095
ohauer search for other commits by this committer
- add stage support
26 May 2014 06:55:07
Original commit files touched by this commit  3.6
Revision:355278
bapt search for other commits by this committer
Convert to USES=dos2unix

With hat:	portmgr
13 Mar 2014 07:41:34
Original commit files touched by this commit  3.6
Revision:348042
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
20 Sep 2013 15:55:44
Original commit files touched by this commit  3.6
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
24 Jul 2012 07:19:21
Original commit files touched by this commit  3.6
cs search for other commits by this committer
Fix typos in COMMENT
19 Mar 2011 12:38:54
Original commit files touched by this commit  3.6
miwi search for other commits by this committer
- Get Rid MD5 support
17 May 2008 16:52:34
Original commit files touched by this commit  3.6
pav search for other commits by this committer
- Update maintainer's email address

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
17 May 2008 16:50:12
Original commit files touched by this commit  3.6
pav search for other commits by this committer
- Try to fix fetch

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
14 May 2008 13:51:50
Original commit files touched by this commit  3.6
pav search for other commits by this committer
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>

Number of commits found: 10

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