UNIT 6.4 Inferring Evolutionary Trees with PAUP*
Published Online: 1 FEB 2003
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
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.
- Published Online: 1 FEB 2003
- 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.