title: MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment.
abstract: As models of sequence evolution become more and more complicated, many criteria for model selection have been proposed, and tools are available to select the best model for an alignment under a particular criterion. However, in many instances the selected model fails to explain the data adequately as reflected by large deviations between observed pattern frequencies and the corresponding expectation. We present MISFITS, an approach to evaluate the goodness of fit (http://www.cibiv.at/software/misfits). MISFITS introduces a minimum number of "extra substitutions" on the inferred tree to provide a biologically motivated explanation why the alignment may deviate from expectation. These extra substitutions plus the evolutionary model then fully explain the alignment. We illustrate the method on several examples and then give a survey about the goodness of fit of the selected models to the alignments in the PANDIT database.
authors.affiliation: Max F Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, Vienna, Austria.
authors.forename: Minh Anh Thi
authors.initials: MA
authors.lastname: Nguyen
authors.forename: Steffen
authors.initials: S
authors.lastname: Klaere
authors.forename: Arndt
authors.initials: A
authors.lastname: von Haeseler
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000032:analysis / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D004272:DNA, Mitochondrial