MISFITS 1.0

MISFITS is a program to evaluate the goodness of fit of a model to an alignment in phylogeny reconstruction. 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.<br />Methods:<br />The method is described in the following article:<br /><br /> * 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., 27, in press. (free copy, DOI: 10.1093/molbev/msq180, PMID: 20643866) <br /><br />A brief description of the method is as follows:<br /><br /> 1. Count the observed frequency of patterns in the alignment.<br /> 2. Compute pattern likelihood under the model and the inferred tree.<br /> 3. Determine the set of over-represented patterns D+ and the set of under-represented patterns D-.<br /> 4. For all pairs of patterns (p, p'), p ???? D+, p' ???? D-, compute the minimal number of extra-substitutions to convert p into p'.<br /> 5. Select a matching between patterns in D+ and D- such that the total number of extra-substitutions is minimal.<br /> 6. Map the extra-substitutions on the tree.<br /> 7. Determine the significance of the number of extra-substitutions computed at step 5.

Requirements:	No special requirements
Platforms:	Mac, Mac OSX
Keyword:	Alignment,  Count,  Determine,  Evaluate,  Extrasubstitutions,  Frequency,  Goodness,  Method,  Minimal,  Misfits,  Model,  Molbevmsq,  Number,  Observed,  Patterns,  Phylogenetic,  Press,  Treemodel
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