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Bioinformatics Advance Access originally published online on December 6, 2005
Bioinformatics 2006 22(6):716-722; doi:10.1093/bioinformatics/bti812
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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In silico sequence evolution with site-specific interactions along phylogenetic trees

Tanja Gesell 1 and Arndt von Haeseler 2,3,4,5,*

1Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1 40225 Duesseldorf, Germany
2Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
3University of Vienna Austria
4Medical University of Vienna Austria
5University of Veterinary Medicine Vienna Austria

*To whom correspondence should be addressed.

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 we introduce a Markov model of nucleotide sequence evolution in which the instantaneous substitution rate at a site depends on the states of other sites. Based on the concept of neighbourhood systems, our model 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 interactions along a tree. For example, we are able to simulate the evolution 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: We implemented our method in an ANSI C program SISSI which runs on UNIX/Linux, Windows and Mac OS systems, including Mac OS X. SISSI is available at http://www.bi.uni-duesseldorf.de/software/sissi/

Contact: sissi{at}cs.uni-duesseldorf.de

Received on July 22, 2005; revised on December 1, 2005; accepted on December 1, 2005

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