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.