| <?xml version="1.0" encoding="UTF-8"?> |
| <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| <pkgmetadata> |
| <herd>sci-biology</herd> |
| <longdescription> |
| 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. |
| </longdescription> |
| </pkgmetadata> |