Unit

UNIT 6.5 Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution

  1. David Posada

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi0605s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Posada, D. 2003. Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution. Current Protocols in Bioinformatics. 00:6.5:6.5.1–6.5.14.

Author Information

  1. Universidad of de Vigo, Vigo, Spain

Publication History

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

Abstract

Models of nucleotide substitution are commonly used in the analysis of DNA sequences. This unit describes the use of the program MODELTEST (coupled with PAUP*) to find the best-fit model of substitution for the sequence alignment at hand. An example data file is analyzed and the interpretation of the results is discussed. Some background theory on model selection and a discussion of the relevance of models is included at the end of the unit.