A new version of the PUZZLE software has been released:
TREE-PUZZLE 5.0
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Heiko A. Schmidt, Heidelberg, Germany.
Korbinian Strimmer, Oxford, UK.
Martin Vingron, Heidelberg, Germany.
Arndt von Haeseler, Leipzig, Germany.
October 2000
http://www.tree-puzzle.de
DESCRIPTION
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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. Branch lengths can also be calculated under the
clock-assumption.
In addition, TREE-PUZZLE offers likelihood mapping, a method
to investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content
of a sequence alignment.
TREE-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-Hasegawa test).
The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG 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.
CHANGES
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What's new in TREE-PUZZLE 5.0:
- Puzzle tree reconstruction part is now parallelized using the MPI standard
(Message Passing Interface).
- Possibility added to specify the names of the input file and the user
tree file at the command line.
Output files renamed to the form PREFIX.EXTENSION, where PREFIX is the
input file name or, if used, the user tree file name.
The EXTENSION could be one of the following: puzzle (PUZZLE report),
tree (tree file), dist (ML distance file), eps (likelihood mapping output
in eps format), qlist (bad quartets), qstep (puzzling step tree IDs as
they occur in the analysis), or qtorder (sorted unique list of puzzling
step trees).
- The tree likelihood value is added to the treefile as a leading comment
("[ lh=x.xxx ]") to the tree string.
- VT (variable time) matrix (Mueller and Vingron, 2000) and WAG matrix
(Whelan and Goldman, 2000) are added to the AA substitution models.
- The Data type and AA-model options in the menu now show the automatically
set type/model first. These can now be changed by using the 'd' or 'm' key
independently from the type/model selected. This makes it possible to
select a desired AA substitution model or data type by piping letters to
the standard input without knowing PUZZLE's preselection.
- Parameters are written to file when estimated before evaluation of the
quartets.
- The inconsistency with respect to other programs in handling invariable
sites has been fixed.
- Some minor bug fixes (e.g. the clockbug and another in the optimization
routine have been fixed).
- Source code organization adopted to the GNU standards
(configure, make, make install under UNIX)
AVAILABILITY
------------
TREE-PUZZLE is available free of charge from
http://www.tree-puzzle.de/ (TREE-PUZZLE home page)
http://www.dkfz-heidelberg.de/tbi/tree-puzzle/ (home page mirror at DKFZ)
or from one of the following places soon
http://iubio.bio.indiana.edu/soft/molbio/evolve (IUBio archive www, USA)
ftp://iubio.bio.indiana.edu/molbio/evolve (IUBio archive ftp, USA)
ftp://ftp.ebi.ac.uk/pub/software (EBI, UK)
ftp://ftp.pasteur.fr/pub/GenSoft (Institut Pasteur, France)
TREE-PUZZLE is written in ANSI C. It will run on most personal computers and
workstations if compiled by an appropriate C compiler. Executables are
available for MacOS and Windows. UNIX and VMS makefiles are also provided.
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Heiko Schmidt
Deutsches Krebsforschungszentrum Tel: + 49 + 6221 / 42-2719
Theoretische Bioinformatik (H0300) Fax: + 49 + 6221 / 42-2849
Im Neuenheimer Feld 280 email: ha.schmidt at web.de
D-69120 Heidelberg URL: http://www.DKFZ-Heidelberg.de/tbi
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