---
name: treepuzzle
version: 5.2
origin: biology/treepuzzle
comment: Maximum likelihood phylogeny reconstruction using quartets
arch: freebsd:9:x86:64
www: http://www.tree-puzzle.de
maintainer: jan.lentfer@web.de
prefix: /usr/local
licenselogic: single
flatsize: 328800
desc: |
  TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from
  molecular sequence data by maximum likelihood. It implements a fast tree search
  algorithm, quartet puzzling, that allows analysis of large data sets and
  automatically assigns estimations of support to each internal branch.
  TREE-PUZZLE also computes pairwise maximum likelihood distances as well as
  branch lengths for user specified trees. Branch lengths can be calculated under
  the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood
  mapping, to investigate the support of a hypothesized internal branch without
  computing an overall tree and to visualize the phylogenetic content of a
  sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on
  the data set (chi-square test for homogeneity of base composition, likelihood
  ratio clock test, Kishino-Hasegawa test). The models of substitution provided by
  TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT,
  WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity
  is modeled by a discrete Gamma distribution and by allowing invariable sites.
  The corresponding parameters can be inferred from the data set.

  WWW: http://www.tree-puzzle.de
categories: [biology]
files:
  /usr/local/bin/puzzle: b87c95a85b67808c3890ff4b6970b10ca1650ab75a1ed3b742d4550be4a6477e
scripts: {}
