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* Update to 3.8.31.Raphael Kubo da Costa2014-06-175-89/+37
| | | | | | | | PR: 191130 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358182
* - add stage supportOlli Hauer2014-06-011-6/+3
| | | | Notes: svn path=/head/; revision=356095
* Convert to USES=dos2unixBaptiste Daroussin2014-05-261-2/+2
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=355278
* - Convert USE_GMAKE to USESMartin Wilke2014-03-131-1/+1
| | | | Notes: svn path=/head/; revision=348042
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-5/+2
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* Fix typos in COMMENTCarlo Strub2012-07-241-1/+1
| | | | Notes: svn path=/head/; revision=301441
* - Get Rid MD5 supportMartin Wilke2011-03-191-3/+0
| | | | Notes: svn path=/head/; revision=271305
* - Update maintainer's email addressPav Lucistnik2008-05-171-1/+1
| | | | | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213206
* - Try to fix fetchPav Lucistnik2008-05-171-0/+2
| | | | | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213205
* MUSCLE is multiple alignment software for protein and nucleotide sequences.Pav Lucistnik2008-05-146-0/+231
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> Notes: svn path=/head/; revision=213031
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