P U Z Z L E
Maximum likelihood analysis for nucleotide and amino acid alignments
Version 3.1
April 1997
Copyright 1995-97 by Korbinian Strimmer and Arndt von Haeseler
Zoologisches Institut, Universitaet Muenchen, Muenchen, Germany
What's new in PUZZLE 3.1:
* Much improved user interface to rate heterogeneity (less confusing
menu, rearranged outfile, additional out-of-range check).
* Possibility to read rooted input trees
(automatic removal of basal bifurcation).
* Computation of average distance between all pairs of sequences.
* Fix of a bug that caused PUZZLE 3.0 to crash on some systems (DEC Alpha).
* Cosmetic changes in program and documentation.
PUZZLE is an application 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. Rate
heterogeneity (invariable sites plus Gamma distributed rates) is
incorporated in all models of substitution available (nucleotides: TN, HKY,
F84, and submodels; amino acids: Dayhoff, JTT, mtREV24). All model
parameters including rate heterogeneity can be estimated from the data by
maximum likelihood. PUZZLE also computes pairwise maximum likelihood
distances as well as branch lengths for user specified trees. In addition,
PUZZLE offers a novel method, likelihood mapping, to investigate the support
of internal branches without computing an overall tree.
PUZZLE is available free of charge from
http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.html (PUZZLE home page)
ftp://ftp.ebi.ac.uk/pub/software (European Bioinformatics Institute)
ftp://ftp.pasteur.fr/pub/GenSoft (Institut Pasteur)
PUZZLE is written as an ANSI C program. This means that it will run on most
personal computers and workstations if compiled by an appropriate C
compiler. Precompiled executables are available for MacOS and MS-DOS. UNIX
and VMS makefiles are also provided.
