muscle 3.6 biology =0

MUltiple Sequence Comparison by Log-Expectation
Maintained by: mzaki@m.u-tokyo.ac.jp
Port Added: 14 May 2008 14:52:50

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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/

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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Required To Build: devel/gmake

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

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Configuration Options

     No options to configure

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Master Sites:

http://www.drive5.com/muscle/downloads3.6/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Update maintainer's email address

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)

- Try to fix fetch

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)

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>

9 vulnerabilities affecting 12 ports have been reported in the past 14 days

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