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Maximum‐Likelihood Analysis Using TREE‐PUZZLE
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 6.6
DOI:
10.1002/0471250953.bi0606s17
Online Posting Date:
March, 2007 Abstract
TREE-PUZZLE provides a means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e., groups of four sequences. Basic Protocol 1 explains how to reconstruct trees based on the maximum-likelihood principle and quartet puzzling. Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol 3 explains how to compare tree topologies using different tests.
Keywords: evolutionary tree; phylogeny reconstruction; tree-puzzle; visualizing phylogenetic content; comparing trees
Table of Contents
- Unit Introduction
- Basic Protocol 1: Reconstruct a Phylogenetic Tree
- Basic Protocol 2: Analyze the Content of Phylogenetic Information and the Quartet Support for the Relationship of Groups of Sequences
- Basic Protocol 3: Compare Tree Topologies
- Support Protocol 1: Obtain and Install TREE-PUZZLE for Unix/Linux and Mac OS X
- Support Protocol 2: Obtain and Install Tree-Puzzle for Mac OS X
- Support Protocol 3: Obtain and Install Tree-Puzzle for MS Windows
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
Figures
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Figure 6.6.1The three possible informative quartet tree topologies. -
Figure 6.6.2Flowchart of analysis type options in the TREE-PUZZLE menu. Options in TREE-PUZZLE are controlled by single letters. The flow chart shows the options that correspond to each letter. For example, entering the letter b toggles the analysis between tree reconstruction and likelihood mapping. Similarly, to choose among quartet puzzling, user-defined trees, or pairwise distance matrices, enter the letter k until the desired option is shown on the screen. -
Figure 6.6.3Flowchart of substitution model options in the TREE-PUZZLE menu. -
Figure 6.6.4Flowchart of further substitution model parameters in the TREE-PUZZLE menu. -
Figure 6.6.5Flowchart of rate heterogeneity options in the TREE-PUZZLE menu. -
Figure 6.6.6Flowchart of parameter estimation options in the TREE-PUZZLE menu. -
Figure 6.6.7TREE-PUZZLE menu setting and screen output from tree reconstruction. -
Figure 6.6.8Phylogenetic tree reconstructed from the EF.phy dataset as described in -
Figure 6.6.9TREE-PUZZLE menu setting and screen output from likelihood-mapping analysis. -
Figure 6.6.10How likelihood weights are plotted in a likelihood-mapping diagram. Left side: likelihood weight plotted in a three-dimensional coordinate system. Right side: the simplex and its areas and the corresponding quartet topologies. The gray triangles are identical, only viewed from different angles. -
Figure 6.6.11Likelihood-mapping diagram visualizing the phylogenetic content of the EF.phy dataset performed as described in -
Figure 6.6.12Likelihood-mapping diagram visualizing the support for a Crenarchaeota-Eukaryota sister group in the EF-2/G genes of the EF.phy dataset as described in -
Figure 6.6.13The three tree topologies used in the usertree comparison. (A) Tree 1: Eukaryota-Crenarchaeota sister groups, (B) Tree 2: Bacteria-Crenarchaeota sister groups, (C) Tree 3: Eukaryota-Bacteria sister groups. The tree topologies are used without branch lengths. -
Figure 6.6.14TREE-PUZZLE menu setting and screen output from usertree evaluation. -
Figure 6.6.15Results of the comparison of three trees from the EF.3trees dataset as described in
Literature Cited
| Literature Cited | |
| Adachi, J. and Hasegawa, M. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459-468. | |
| Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. 1978. A model of evolutionary change in proteins. In Atlas of Protein Sequence Structure, Vol. 5 (M.O. Dayhoff, ed.) pp. 345-352. National Biomedical Research Foundation, Washington, D.C. | |
| Edwards, A.W.F. and Cavalli-Sforza, L.L. 1964. Reconstruction of evolutionary trees. In Phenetic and Phylogenetic Classification (V.H. Heywood and J. McNeill, eds.) pp. 67-76. Systematics Association, London. | |
| Felsenstein, J. 1978. The number of evolutionary trees. Syst. Zool. 27:27-33. | |
| Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376. | |
| Felsenstein, J. 1984. Distance methods for inferring phylogenies: A justification. Evolution 38:16-24. | |
| Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Mass. | |
| Goldman, N. 1993a. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198. | |
| Goldman, N. 1993b. Simple diagnostic statistical tests of models for DNA substitution. J. Mol. Evol. 37:650-661. | |
| Goldman, N., Anderson, J.P., and Rodrigo, A.G. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670. | |
| Gu, X., Fu, Y.-X., and Li, W.-H. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557. | |
| Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174. | |
| Henikoff, S. and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89:10915-10919. | |
| Hillis, D.M. 1996. Inferring complex phylogenies. Nature 383:130-131. | |
| Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S., and Miyata, T. 1989. Evolutionary relationship of Archaebacteria, Eubacteria, and Eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. U.S.A. 86:9355-9359. | |
| Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282. | |
| Jukes, T.H. and Cantor, C.R. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism (H.N. Munro, ed.). Academic Press, New York. | |
| Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. | |
| Kishino, H. and Hasegawa, M. 1989. Evolution of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179. | |
| Lanave, C., Preparata, G., Saccone, C., and Serio, G. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93. | |
| McMorris, F.R. and Neumann, D.A. 1983. Consensus functions defined on trees. Math. Soc. Sci. 4:131-136. | |
| Müller, T. and Vingron, M. 2000. Modeling amino acid replacement. J. Comput. Biol. 7:761-776. | |
| Page, R.D. and Holmes, E.C. 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell Science, Oxford. | |
| Posada, D. and Crandall, K.A. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818. | |
| Posada, D. and Buckley, T. 2004. Model selection and model averaging in phylogenetics: Advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808. | |
| Sanderson, M.J. and Shaffer, H.B. 2002. Troubleshooting molecular phylogenetic analyses. Annu. Rev. Ecol. Syst. 33:49-72. | |
| Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. | |
| Schöniger, M. and von Haeseler, A. 1994. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phyl. Evol. 3:240-247. | |
| Shimodaira, H. and Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116. | |
| Strimmer, K. and von Haeseler, A. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969. | |
| Strimmer, K. and von Haeseler, A. 1997. Likelihood mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. U.S.A. 94:6815-6819. | |
| Strimmer, K. and Rambaut, A. 2002. Inferring confidence sets of possibly misspecified gene trees. Proc. R. Soc. Lond. B 269:137-142. | |
| Strimmer, K., Goldman, N., and von Haeseler, A. 1997. Bayesian probabilities and quartet puzzling. Mol. Biol. Evol. 14:210-213. | |
| Swofford, D.L., Olsen, G.J., Waddell, P.J., and Hillis, D.M. 1996. Phylogeny reconstruction. In Molecular Systematics, 2nd ed. (D.M. Hillis, C. Moritz, and B.K. Mable, eds.) pp. 407-514. Sinauer Associates, Sunderland, Mass. | |
| Tamura, K. and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526. | |
| Tavare, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lec. Math. Life Sci. 17:57-86. | |
| Whelan, S. and Goldman, N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Mol. Biol. Evol. 18:691-699. | |
| Key References | |
| Felsenstein, 2004. See | |
| A comprehensive textbook covering almost all areas of phylogenetic inference. | |
| Goldman et al., 2000. See | |
| A comprehensive review discussing tests for tree topologies and their applicability. | |
| Page and Holmes, 1998. See | |
| A well written textbook about phylogenetics and its applications. | |
| Sanderson and Shaffer, 2002. See | |
| A good review on problems in phylogeny reconstruction. | |
| Strimmer and von Haeseler, 1996. See | |
| An original publication of the Quartet Puzzling method. | |
| Strimmer and von Haeseler, 1997. See | |
| A more detailed description of Likelihood Mapping. | |
| Swofford et al., 1996. See | |
| An excellent introduction to the rich collection of phylogenetic methods. | |
| Internet Resources | |
| http://www.tree-puzzle.de | |
| TREE-PUZZLE Web site. | |
| http://rdp8.cme.msu.edu/download/programs/TreeTool/ | |
| TreeTool Web site (tree-drawing program). | |
| http://taxonomy.zoology.gla.ac.uk/rod/treeview.html | |
| TreeView Web site (tree-drawing program, see unit | |
| http://evolution.genetics.washington.edu/phylip/software.html | |
| Joe Felsenstein's list of tree-reconstruction and -drawing programs. | |
| http://www.ghostscript.com/ | |
| GhostScript Web page (PostScript viewer and converter). | |
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