Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
- 1 January 2003
- journal article
- Published by Wiley in Current Protocols in Bioinformatics
- Vol. 00 (1), Unit 6.5
- https://doi.org/10.1002/0471250953.bi0605s00
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.Keywords
This publication has 49 references indexed in Scilit:
- Different Models, Different Trees: The Geographic Origin of PTLV-IMolecular Phylogenetics and Evolution, 1999
- Postglacial connection of the Black Sea to the Mediterranean and its relation to the timing of sapropel formationPaleoceanography and Paleoclimatology, 1997
- How often do wrong models produce better phylogenies?Molecular Biology and Evolution, 1997
- Among-site rate variation and its impact on phylogenetic analysesTrends in Ecology & Evolution, 1996
- Robustness of maximum likelihood tree estimation against different patterns of base substitutionsJournal of Molecular Evolution, 1991
- The general stochastic model of nucleotide substitutionJournal of Theoretical Biology, 1990
- Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution, 1981
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution, 1980
- A new look at the statistical model identificationIEEE Transactions on Automatic Control, 1974
- On Information and SufficiencyThe Annals of Mathematical Statistics, 1951