---
name: phyml
version: 20121109
origin: biology/phyml
comment: Simple, fast, and accurate algorithm to estimate large phylogenies
arch: freebsd:9:x86:64
www: http://code.google.com/p/phyml/
maintainer: ports@FreeBSD.org
prefix: /usr/local
licenselogic: single
licenses: [GPLv2]
flatsize: 1010737
desc: "PhyML is a software that estimates maximum likelihood phylogenies from \nalignments
  of nucleotide or amino acid sequences. It provides a wide range of\noptions that
  were designed to facilitate standard phylogenetic analyses. The\nmain strengths
  of PhyML lies in the large number of substitution models coupled\nto various options
  to search the space of phylogenetic tree topologies, going\nfrom very fast and efficient
  methods to slower but generally more accurate\napproaches. It also implements two
  methods to evaluate branch supports in a\nsound statistical framework (the non-parametric
  bootstrap and the approximate\nlikelihood ratio test). PhyML was designed to process
  moderate to large data\nsets. In theory, alignments with up to 4,000 sequences 2,000,000
  character-long\ncan analyzed. In practice however, the amount of memory required
  to process a\ndata set is proportional of the product of the number of sequences
  by their\nlength. Hence, a large number of sequences can only be processed provided
  that\nthey are short. Also, PhyML can handle long sequences provided that they are\nnot
  numerous. With most standard personal computers, the \"comfort zone\" for\nPhyML
  generally lies around 3 to 500 sequences less than 2,000 character long.\n\nWWW:
  http://code.google.com/p/phyml/\n"
categories: [biology]
files:
  /usr/local/bin/phyml: 50c06ecdf53817f0c37643ef71a459ca958a8305d458ff8aaf06f50db23b14df
  /usr/local/share/licenses/phyml-20121109/GPLv2: 8177f97513213526df2cf6184d8ff986c675afb514d4e68a404010521b880643
  /usr/local/share/licenses/phyml-20121109/LICENSE: 7e1394d03c5f275a402fe721ff1d1349449ea8602b52af954c76463afcdb6ef7
  /usr/local/share/licenses/phyml-20121109/catalog.mk: 5d06417137d5973884c306e2f4c7030c9c81774a4b533fc04ac56df178783a2b
directories:
  /usr/local/share/licenses/phyml-20121109/: n
  /usr/local/share/licenses/: y
scripts:
  post-install: |
    cd /usr/local
  pre-deinstall: |
    cd /usr/local
  post-deinstall: |
    cd /usr/local
