Reconstruction of phylogenetic trees by maximum likelihood (doc)

 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