One step mutation matrices: A fresh view on modeling sequence evolution

29/05/2012 - Room C209 at 14:00 - External Seminar
Prof. Arndt von Haeseler
(Center for Integrative Bioinformatics Vienna (CIBIV))
As models of sequence evolution become more and more complicated, many criteria for model selection have been pro- posed, 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 pat- tern frequencies and the corresponding expectation. We present MISFITS, an approach to evaluate the goodness of fit. 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. Moreover, we illustrate how the number of extra substitutions may be used to study robustness in phylogenetic inference. We therefore introduce ImOSM, a tool to imbed intermittent evolution as model violation into an alignment. Intermittent evolution refers to extra substitutions occurring randomly on branches of a tree, thus changing alignment site patterns. This means that the extra substitutions are placed on the tree after the typical process of sequence evolution is completed.
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