Selecting a model of nucleotide substitution

Models of nucleotide substitution are commonly used in the analysis of DNA sequences. In this unit a protocol is described for 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. Choosing the best-fit model of nucleotide substitution Models of nucleotide substitution are commonly used in the analysis of DNA sequences, especially in the estimation of evolutionary parameters and in the construction of phylogenetic trees. A common problem that a researcher has to face is the objective selection of such a sample. The program MODELTEST (Posada and Crandall, 1998) offers two sound statistical procedures to carry out this choice. This protocol describes the joint use of the program MODELTEST and PAUP* (Swofford, 2000) to select the best-fit model of nucleotide substitution for a given set of aligned DNA sequences. The three basic steps within this protocol consist of the estimation of a phylogenetic tree, the estimation of likelihood scores for the candidate models, and the selection of a particular model given these likelihood scores. The first two procedures are carried in the program PAUP* with a batch file included in the MODELTEST package. The discussion in this unit summarizes the theory behind the procedure and provides several caveats and guides for interpretation of the results. Particular comments about the implementation different platforms are also given. Users are encouraged to download the most current versions from the MODELTEST and PAUP* Web site USING MODELTEST AND PAUP* TO SELECT A MODEL OF NUCLEOTIDE SUBSTITUTION