Inferring Evolutionary Trees with PAUP*

James C. Wilgenbusch1, David Swofford1

1 Florida State University, Tallahassee, Florida
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 6.4
DOI:  10.1002/0471250953.bi0604s00
Online Posting Date:  February, 2003
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Abstract

This unit provides a general description of reconstructing evolutionary trees using PAUP* 4.0. The protocol takes users through an example analysis of mitochondrial DNA sequence data using the parsimony and the likelihood criteria to infer optimal trees. The protocol also discusses searching options available in PAUP* and demonstrates how to import non‐NEXUS formats. Finally, a general discussion is given regarding the pros and cons of the “model‐free” and “model‐based” methods used throughout the protocol.

     
 
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Table of Contents

  • Basic Protocol 1: Using PAUP* to Infer Parsimony Trees from DNA Sequences
  • Alternate Protocol 1: Using PAUP* to Infer a Maximum‐Likelihood Tree from DNA Sequences
  • Support Protocol 1: Using PAUP* to Import Non‐NEXUS Data Files
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
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   Swofford, D.L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Mass.
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   Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.J., Lewis, P.O., and Rogers, J.S. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525‐539.
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   Yang, Z. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306‐314.
Internet Resources
   http://paup.csit.fsu.edu/
  PAUP* Web site.
   http://pauptech.csit.fsu.edu/∼paupforum/
  PAUP* technical forum.
   http://mailer.csit.fsu.edu/mailman/listinfo/paupinfo/
  PAUP* information mailing list.
   http://www.sinauer.com/
  PAUP* publisher, Sinauer Associates, Inc. Web site.
Key References
   Hillis et al., 1996. See above.
  A general discussion of issues and controversies pertaining to phylogenetic analyses.
   Page and Holmes, 1998. See above.
  An accessible introduction to phylogenetic theory, terminology, and practice.
   Swofford et al., 1996. See above.
  A detailed description of most methods commonly used in phylogenetic inference.
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