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Diffstat (limited to 'biology/treepuzzle/pkg-descr')
| -rw-r--r-- | biology/treepuzzle/pkg-descr | 18 |
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diff --git a/biology/treepuzzle/pkg-descr b/biology/treepuzzle/pkg-descr new file mode 100644 index 000000000000..1e51ea40d926 --- /dev/null +++ b/biology/treepuzzle/pkg-descr @@ -0,0 +1,18 @@ +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 |