---
name: muscle
version: 3.6
origin: biology/muscle
comment: Multiple Sequence Comparison by Log-Expectation
arch: freebsd:9:x86:64
www: http://www.drive5.com/muscle/
maintainer: mzaki@m.u-tokyo.ac.jp
prefix: /usr/local
licenselogic: single
flatsize: 879620
desc: |
  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/
categories: [biology]
files:
  /usr/local/bin/muscle: 6b661d32b86e6e3cb6384b4e31651977749e7fab4fbc1e41e3ffc147068de620
  /usr/local/share/doc/muscle/muscle.html: 4df43445f08d99e18da71a06438cc8fc3ba42b6709e19c8cfea0c31788dc17b6
  /usr/local/share/doc/muscle/muscle.pdf: a28fd0afc0919c176a9a1cedb3b46cadb24a53c575089305cc4b2967ec4a5fc9
directories:
  /usr/local/share/doc/muscle/: n
scripts: {}
