Using <scp>MODELTEST</scp> and <scp>PAUP</scp>* to Select a Model of Nucleotide Substitution

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.