Tree-puzzle (the new name for puzzle) is an interactive console program that 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 also 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.

this is the documentation package for tree-puzzle