UNIT 6.4 Inferring Evolutionary Trees with PAUP*

  1. James C. Wilgenbusch,
  2. David Swofford

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi0604s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Wilgenbusch, J. C. and Swofford, D. 2003. Inferring Evolutionary Trees with PAUP*. Current Protocols in Bioinformatics. 00:6.4:6.4.1–6.4.28.

Author Information

  1. Florida State University, Tallahassee, Florida

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: JAN 2003


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.