misfits is a computer program to evaluate the goodness of fit between a phylogenetic model and an alignment.It offers a look back at the alignment to pinpoint to site patterns that do not fit to the model and the resulting tree (thereafter referred to as the tree-model). MISFITS then introduces a number of extra-substitutions on the tree, in a parsimonious manner to fit these site patterns in to the tree-model. These extra-substitutions plus the evolutionary model will then fully explain the alignment. Thus, the number of extra-substitutions may be interpreted as a measure to evaluate the goodness of fit of the model to the alignment: the less the number, the better the fit.
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Minh Anh Thi Nguyen, Steffen Klaere, and Arndt von Haeseler (2010)
MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment.
Mol. Biol. Evol., 28:143-152.