Phylogenetics In silico sequence evolution with site-specific interactions along phylogenetic trees

Motivation: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here weintroduceaMarkovmodelofnucleotidesequenceevolutioninwhich the instantaneous substitution rate at a site depends on the states of othersites.Basedontheconceptofneighbourhoodsystems,ourmodel represents a universal description of arbitrarily complex dependencies among sites. Results: We show how to define complex models for some illustrative examples and demonstrate that our method provides a versatile resource for simulations of sequence evolution with site-specific inter-actionsalong atree.Forexample,weare ableto simulatetheevolution of RNA taking into account both secondary structure as well as pseudoknots and other tertiary interactions. To this end, we have developed a program Simulating Site-Specific Interactions (SISSI) that simulates evolution of a nucleotide sequence along a phylogenetic tree incorporating user defined site-specific interactions. Furthermore, our method allows to simulate more complex interactions among nucleotide and other character based sequences. Availability:

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