PhyML is a software that estimates maximum likelihood phylogenies from 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. Fix: See attached shar. Patch attached with submission follows:
Responsible Changed From-To: freebsd-ports-bugs->amdmi3 I'll take it.
State Changed From-To: open->feedback Does not build (http://people.freebsd.org/~amdmi3/phyml-20090706.log), apparently because it misses depends on autotools. You should use USE_AUTOTOOLS instead (this both depend on and call autotools for you). In either case, don't use scripts/.
Here is a new version using USE_AUTOTOOLS. Let me know if there is any other best practices that I've missed. See attached shar.
State Changed From-To: feedback->open Submitter has fixed.
State Changed From-To: open->closed New port added, with minor changes. Thanks!
amdmi3 2009-07-21 01:10:13 UTC FreeBSD ports repository Modified files: biology Makefile Added files: biology/phyml Makefile distinfo pkg-descr biology/phyml/files patch-src-configure patch-src-configure.ac Log: PhyML is a software that estimates maximum likelihood phylogenies from 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> Revision Changes Path 1.111 +1 -0 ports/biology/Makefile 1.1 +31 -0 ports/biology/phyml/Makefile (new) 1.1 +3 -0 ports/biology/phyml/distinfo (new) 1.1 +11 -0 ports/biology/phyml/files/patch-src-configure (new) 1.1 +11 -0 ports/biology/phyml/files/patch-src-configure.ac (new) 1.1 +18 -0 ports/biology/phyml/pkg-descr (new) _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"