Description:

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.
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.