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TREE-PUZZLE:
Maximum likelihood analysis for nucleotide, amino acid, and two-state
data
Copyright 2005-2015 by Heiko A. Schmidt
and Arndt von Haeseler
Copyright 2003-2004 by Heiko A. Schmidt,
Korbinian Strimmer,
and Arndt von Haeseler
Copyright 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, and Arndt von Haeseler
Copyright 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
News
- Finally, also packages with executables for different operating systems for pre-release TREE-PUZZLE 5.3.rc16 have been added.
- A pre-release version TREE-PUZZLE 5.3.rc16 has been made available.
- A book chapter about ML-based testing of tree topologies using TREE-PUZZLE and Consel has been published (April 2009):
H.A. Schmidt (2009)
Testing Tree Topologies.
In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 381-404, Cambridge University Press, Cambridge.
(ISBN: paperback: 9780521730716, hardcover: 9780521877107, datasets at www.thephylogenetichandbook.org)
- A book chapter about ML-based tree reconstruction using TREE-PUZZLE, IQPNNI and other methods has been published (April 2009):
H.A. Schmidt and A. von Haeseler (2009)
Phylogenetic Inference Using Maximum Likelihood Methods.
In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 181-209, Cambridge University Press, Cambridge.
(ISBN: paperback: 9780521730716, hardcover: 9780521877107, datasets at www.thephylogenetichandbook.org)
- An updated CPBI unit about TREE-PUZZLE has been published (March 2007):
Schmidt, H.A. and A. von Haeseler (2007)
Maximum-Likelihood Analysis Using TREE-PUZZLE.
In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.)
Current Protocols in Bioinformatics (Supplement 17),
Unit 6.6, Wiley and Sons, New York.
(DOI: 10.1002/0471250953.bi0606s17,
PMID: 18428792,
ISBN 0-471-25093-7,
CP online)
- A book chapter on the application of parallel parameter estimation on heterogeneous workstation clusters (May 2006):
E. Petzold, D. Merkle, M. Middendorf, A. von Haeseler, and H.A. Schmidt (2006)
Phylogenetic Parameter Estimation on COWs.
In A.Y. Zomaya (ed.)
Parallel Computing for Bioinformatics and Computational Biology,
347-368, Wiley and Sons, New York.
(ISBN 0-471-71848-3)
- An article about the parallel performance parallel TREE-PUZZLE (October 2003):
Schmidt, H.A., E. Petzold, M. Vingron, and A. von Haeseler (2003)
Molecular Phylogenetics: Parallelized Parameter Estimation and Quartet Puzzling.
J. Parallel Distrib. Comput., 63, 719-727.
(DOI: 10.1016/S0743-7315(03)00129-1)
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. TREEPUZZLE also computes pairwise maximum likelihood
distances as well as branch lengths for user specified trees.
Branch lengths can be calculated with and without the molecular-clock
assumption. In addition, TREE-PUZZLE o ers 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, one and two-sided
Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood
Weights). The models of substitution provided by TREE-PUZZLE are GTR, 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 modeled
by a discrete Gamma distribution and by allowing invariable sites.
The corresponding parameters (except for GTR) can be inferred from the
data set.
Also available from this site:
PUZZLEBOOT by Mike Holder and Andrew Roger
(PUZZLEBOOT main site).
Download current version
An updated version of TREE-PUZZLE (5.3.rc) is available as a pre-release to the upcomming version 5.3.
To download the software your web browser has to be properly configured
to recognize the file extensions. (In most browsers you should be able to
clicking with right mouse button and select "save link".)
New features in version 5.3 include
- Likelihood mapping output in SVG format
- An interface to enter commandline parameters if started by double-click (the executable has to be renamed to contain 'clicky', e.g. puzzle-clicky.exe)
- Evaluation of parsimony-informative sites for the alignment using an extended definition of parsimony-informativeness.
- Evaluation of parsimony-informative sites per sequence.
- Stop after alignment evaluation with the flag -statsonly.
- LG model of protein evolution added.
- Perform a relative majority consensus with -consmrel.
- Write pairwise edit distances to PREFIX.editdist with -weditdist.
- Write pairwise substitutions counts to PREFIX.tstv with -wtstv.
- Write splits file PREFIX.splits with -wsf.
- Write splits in nexus format with -wsnex.
- Write site rates to PREFIX.siterate with -wsr.
- Write site log-likelihoods to PREFIX.sitelh (PHILIP-like format) with -wsl.
- Write intermediate trees in nexus format with -witnex.
- Furthermore, a few issues with larger datasets have been fixed.
- Consensus tree construction for user given sets of trees (providing
50% majority and relative majority consensus, cf.
manual for details. Was already in 5.2)
References and Publications
- If you intend to use TREE-PUZZLE in a publication please cite the program as
Schmidt, H.A., K. Strimmer, M. Vingron, and A. von Haeseler (2002)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and
parallel computing. Bioinformatics. 18:502-504.
(DOI: 10.1093/bioinformatics/18.3.502,
PMID: 11934758)
- For the quartet puzzling algorithm please use:
Strimmer, K., and A. von Haeseler (1996) Quartet puzzling:
A quartet maximum likelihood method for reconstructing tree topologies.
Mol. Biol. Evol. 13: 964-969.
(journal page)
- For likelihood mapping please use:
Strimmer, K., and A. von Haeseler (1997) Likelihood-mapping: A
simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA. 94:6815-6819.
(PMID: 9192648)
- For the quartet selection taking into account 2nd and 3rd best quartets:
Strimmer, K., N. Goldman and A. von Haeseler (1997) Bayesian Probabilities and Quartet Puzzling. Mol. Biol. Evol. 14:210-213.
(journal page)
- For the current parallel version of TREE-PUZZLE please use:
Schmidt, H.A., K. Strimmer, M. Vingron, and A. von Haeseler (2002)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and
parallel computing. Bioinformatics. 18:502-504.
(DOI: 10.1093/bioinformatics/18.3.502,
PMID: 11934758)
- Hands-on excercises and explainations of features and usage of TREE-PUZZLE can be found in:
Schmidt, H.A. and A. von Haeseler (2007)
Maximum-Likelihood Analysis Using TREE-PUZZLE.
In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.)
Current Protocols in Bioinformatics (Supplement 17),
Unit 6.6, Wiley and Sons, New York.
(DOI: 10.1002/0471250953.bi0606s17,
PMID: 18428792,
ISBN 0-471-25093-7,
CP online)
H.A. Schmidt and A. von Haeseler (2009)
Phylogenetic Inference Using Maximum Likelihood Methods.
In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 181-209, Cambridge University Press, Cambridge.
(ISBN: paperback: 9780521730716, hardcover: 9780521877107)
H.A. Schmidt (2009)
Testing Tree Topologies.
In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 381-404, Cambridge University Press, Cambridge.
(ISBN: paperback: 9780521730716, hardcover: 9780521877107)
- Further details about TREE-PUZZLE can be found in:
H.A. Schmidt (2003) Phylogenetic Trees from Large Datasets.
PhD Thesis, Düsseldorf University, Germany.
(available from Düsseldorf University E-Diss server or as local copy)
Korbinian Strimmer (1997) Maximum likelihood methods in molecular phylogenetics.
PhD Thesis, Munich University, Germany.
(manuscript available from Korbinian Strimmer's Lab)
E. Petzold, D. Merkle, M. Middendorf, A. von Haeseler, and H.A. Schmidt (2006)
Phylogenetic Parameter Estimation on COWs.
In A.Y. Zomaya (ed.)
Parallel Computing for Bioinformatics and Computational Biology,
347-368, Wiley and Sons, New York.
(ISBN 0-471-71848-3)
Distribution site
The most up-to-date version of the TREE-PUZZLE program is distributed at
In addition, binary distributions can be found at
(these are possibly older versions)
Previous Versions
For "historical" reasons (e.g., to allow cross-checks of older results)
we keep previous versions of PUZZLE available.
As the sources and documentation are identical across different platforms
only gzipped tar archives are provided.
Related Software (in alphabetical order)
- consel
consel
(by Hidetoshi Shimodaira & Masami Hasegawa)
for assessing the confidence of phylogenetic tree selection
based on partial likelihoods, e.g., output by tree-puzzle using the '-wsl' option.
- covARES
covARES
(by Christian Blouin) allows to map site rates extracted from a
tree-puzzle output file into a PDB protein structure.
The resulting PDB files have their beta and occupancy fields
mapped with the specified values.
-
PUZZLEBOOT
Michael E. Holder (holder(AT)uh.edu) from the High
Performance Computing Center of the University of Houston
and Andrew J. Roger (aroger(AT)is.dal.ca) from
the Department of Biochemistry and Molecular Biology
of Dalhousie University are distributing a
shell-script program called "puzzleboot" that allows the
analysis of multiple data sets with PUZZLE even though PUZZLE
lacks the "M" option of many PHYLIP programs. It is designed
for use with the distance matrix option of PUZZLE.
PUZZLEBOOT is available from the
PUZZLEBOOT main site
or from this site (download the
README file and the
puzzleboot v1.03 script).
Acknowledgment:
PUZZLEBOOT was originally conceived and developed while both
authors were in the employ of Mitch Sogin at the
Marine Biological Laboratory, Woods Hole, MA 02543 USA.
Contact
- Heiko A. Schmidt
- email: heiko.schmidt(AT)univie.ac.at,
Center for Integrative Bioinformatics Vienna (CIBIV),
Max F. Perutz Laboratories (MFPL),
A-1030 Vienna, Austria.
- Arndt von Haeseler
- email: arndt.von.haeseler(AT)univie.ac.at,
Center for Integrative Bioinformatics Vienna (CIBIV),
Max F. Perutz Laboratories (MFPL),
A-1030 Vienna, Austria.
Imprint of CIBIV
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