Abstract
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.
Keywords
Protocol (science)Computer scienceNexus (standard)Tree (set theory)BiologyEvolutionary biologyComputational biologyMathematicsCombinatorics
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Publication Info
- Year
- 2003
- Type
- article
- Volume
- 00
- Issue
- 1
- Pages
- Unit 6.4-Unit 6.4
- Citations
- 391
- Access
- Closed
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Cite This
James C. Wilgenbusch,
David L. Swofford
(2003).
Inferring Evolutionary Trees with <scp>PAUP</scp>*.
Current Protocols in Bioinformatics
, 00
(1)
, Unit 6.4-Unit 6.4.
https://doi.org/10.1002/0471250953.bi0604s00
Identifiers
- DOI
- 10.1002/0471250953.bi0604s00