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Bioinformatics Advance Access published online on December 6, 2005
Bioinformatics, 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
Received July 22, 2005
Revised December 1, 2005
Accepted December 1, 2005

Article

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

Tanja Gesell 1 and Arndt von Haeseler 2 *

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

* To whom correspondence should be addressed.
Arndt von Haeseler, E-mail: sissi{at}cs.uni-duesseldorf.de


  Abstract

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 (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/.


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