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* - Stage supportMartin Wilke2014-01-311-1/+0
| | | | Notes: svn path=/head/; revision=341987
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-0/+1
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - Remove MAKE_JOBS_SAFE variableAlex Kozlov2013-08-141-1/+0
| | | | | | | Approved by: portmgr (bdrewery) Notes: svn path=/head/; revision=324744
* - Update to 20121109.Marcelo Araujo2013-02-044-43/+25
| | | | | | | | PR: ports/175014 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Notes: svn path=/head/; revision=311601
* - Reset MAINTAINER due to unrecoverable email bounceRyan Steinmetz2012-12-041-1/+1
| | | | | | | | Reported by: portscout Feature safe: yes Notes: svn path=/head/; revision=308268
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* Sync to new bsd.autotools.mkAde Lovett2010-12-041-1/+1
| | | | Notes: svn path=/head/; revision=265663
* Round one migration of ports from automake{19,110} to automake111Ade Lovett2010-10-051-1/+1
| | | | Notes: svn path=/head/; revision=262460
* PhyML is a software that estimates maximum likelihood phylogenies fromDmitry Marakasov2009-07-215-0/+74
alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. WWW: http://code.google.com/p/phyml/ PR: 136877 Submitted by: Ben Allen <ben@sysadminschronicles.com> Notes: svn path=/head/; revision=238140