P U Z Z L E
Maximum likelihood analysis for nucleotide and amino acid alignments
Version 3.0
March 1997
Copyright 1995-97 by Korbinian Strimmer and Arndt von Haeseler
Zoologisches Institut, Universitaet Muenchen, Muenchen, Germany
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
heterogenity (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
and
ftp://ftp.ebi.ac.uk/pub/software/ (archives will be updated soon)
The online manual can be viewed at
http://www.zi.biologie.uni-muenchen.de/~strimmer/manual.html
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.
What's new in PUZZLE 3.0:
* Rate heterogenity included in all models of substitution (Gamma
distribution plus invariable sites).
* Likelihood mapping analysis with Postscript output.
* Much more sophisticated maximum likelihood parameter estimation
for all model parameters including those of rate heterogenity.
* Codon positions selectable. Update to mtREV24. Less verbose runtime
messages. HTML documentation. Better internal error classification.
More information in outfile (number of constant postions etc.).
