---
name: paml
version: 4.4c
origin: biology/paml
comment: Phylogenetic Analysis by Maximum Likelihood (PAML)
arch: freebsd:9:x86:64
www: http://abacus.gene.ucl.ac.uk/software/paml.html
maintainer: wen@FreeBSD.org
prefix: /usr/local
licenselogic: single
flatsize: 2437314
desc: "Phylogenetic Analysis by Maximum Likelihood (PAML)\n\nPAML is a program package
  for phylogenetic analyses of DNA or protein\nsequences using maximum likelihood,
  and is maintained and distributed\nby Ziheng Yang. \n\nPossible uses of the programs
  are:\n- Estimation of branch lengths in a phylogenetic tree and parameters\n  in
  the evolutionary model such as the transition/transversion rate\n  ratio, the shape
  parameter of the gamma distribution for variable\n  evolutionary rates among sites,
  and rate parameters for different\n  genes;\n- Test of hypotheses concerning sequence
  evolution, such as rate\n  constancy and independence among nucleotide or amino
  acid sites, rate\n  constancy among lineages (the molecular clock), and homogeneity
  of\n  evolutionary process in multiple genes;\n- Calculation of substitution rates
  at sites; \n- Reconstruction of ancestral nucleotide or amino acid sequences;\n-
  Simulation of nucleotide, codon, and amino acid sequence data sets; \n- Phylogenetic
  tree reconstruction by maximum likelihood and Bayesian methods. \n\nWWW: http://abacus.gene.ucl.ac.uk/software/paml.html\n"
categories: [biology]
files:
  /usr/local/bin/baseml: d9a29138ab3ed05a40145a3b0dcba73253784547411f6318236786c7ecbcb7b5
  /usr/local/bin/basemlg: f52b5a0b7b31745dfe07f62b0a2f218c266bbdffe42cfc6e37f5409abe5f3c8b
  /usr/local/bin/chi2: 837c4de8b22a3fed8d75484f84291dcad0e071cf1b48ba2ed0c2df4277c5530f
  /usr/local/bin/codeml: c40ac8021c0696d1da29b86565f172baed35f46d2def817b5f24b6f4b0bf6cdb
  /usr/local/bin/evolver: b475aecf6ff9387b725b2999ddc6eab3966aea0c3c7dad7d75284cf7e996a506
  /usr/local/bin/pamp: c3973ae4bc066acc14a2169cd8c05afbb877415842408aca7f5fc828e25d98ef
  /usr/local/bin/yn00: 0dab5e4d698e46b268433cd6a095cfa1472445ab2758164837988582a22bdeb7
  /usr/local/share/doc/paml/MCMCtreeDoc.pdf: 5d8f546f21ab63026adeff11ca762c54855251b473c07507d440065c51b406d2
  /usr/local/share/doc/paml/pamlDOC.pdf: 1138a016a81f22e404ecc5115134e03d0ae284bef0d011b588dab3a5a28643f3
  /usr/local/share/doc/paml/pamlFAQs.pdf: 00446c5bf580e820f5431e07b9b096bc175a953de1caa14eeec8c4837d87b786
  /usr/local/share/doc/paml/pamlHistory.txt: 1174ee048a9542a65c61fd911b6089edae136db37ee5486da0a99a0034c316bf
directories:
  /usr/local/share/doc/paml/: n
scripts: {}
