biology/puzzle 5.2nb2 NetBSD

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. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, 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. PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, Kishino-Hasegaw a test). The models of substitution provided by PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modelled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.