FreshPorts -- The Place For Ports If you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter

I am looking for an LTO tape library. Do you have one to spare?
Port details
muscle 3.8.31 biology on this many watch lists=0 search for ports that depend on this port
MUltiple Sequence Comparison by Log-Expectation
Maintained by: 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 : Main Web Site : 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

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

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

This site
What is FreshPorts?
About the authors
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
flacNov 25
asterisk11Nov 21
asterisk11Nov 21
phpmyadminNov 21
kde4-runtimeNov 20
kwebkitpartNov 20
yiiNov 19
chromiumNov 18
kde4-workspaceNov 17
dbusNov 11
wgetNov 08
konversation-kde4Nov 05
jenkinsOct 31
jenkins-ltsOct 31
twikiOct 31

9 vulnerabilities affecting 11 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds


Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 24384
Broken 140
Deprecated 74
Ignore 397
Forbidden 1
Restricted 206
No CDROM 93
Vulnerable 18
Expired 12
Set to expire 70
Interactive 0
new 24 hours 2
new 48 hours4
new 7 days50
new fortnight174
new month231

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2014 Dan Langille. All rights reserved.