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TREE-PUZZLE
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Imprint
TREE-PUZZLE:
Maximum likelihood analysis for nucleotide, amino acid, and two-state data

Copyright 2003-2011 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

  • 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)

  • TREE-PUZZLE 5.2 has been released (July 2004). This release contains a number of extensions and bug fixes. Older versions should not be used any more. There are executables available for Linux, Windows, and MacOSX.

  • 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

The current version of TREE-PUZZLE is 5.2. It was released in July 2004. A complete list of its features as well as installation instructions are given in the manual (tree-puzzle.pdf).

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".)
Detailed features and instructions are given in the manual (PDF) which is included in all distributions.

New features in version 5.2 include

  • Significantly faster implementation of the puzzling step.
  • GTR model
  • Consensus tree construction for user given sets of trees (providing 50% majority and relative majority consensus, cf. manual for details.)
  • The upper limit of 257 is gone for likelihood mapping, usertree evaluation, consensus construction, and parameter estimation. Parameter estimation, tree evaluation, can also be done for three sequences.
  • Parallel parameter estimation.
  • Several bugs fixed: A bug that tended to make trees reconstructed less resolved has been rectified. The KH tests have been altered to not artificially reject a tree if the variance between it and the best tree is too small. WAG matrix data has been corrected. A number of further minor bugs.

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)

buttonconsel

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 iconcovARES

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 icon 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