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Inferring models of rearrangements, recombinations, and horizontal transfers by the minimum evolution criterion
KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
2007 (English)In: Algorithms in Bioinformatics, Proceedings / [ed] Giancarlo, R; Hannenhalli, S, 2007, Vol. 4645, 111-123 p.Conference paper (Refereed)
Abstract [en]

The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements, and horizontal transfer of genetic material. Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. Since contemporary methods for inferring phylogenetic networks require aligned sequences as input, they cannot deal with viral evolution. In this work we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution, investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as biological datasets.

Place, publisher, year, edition, pages
2007. Vol. 4645, 111-123 p.
, Lecture Notes in Bioinformatics, ISSN 0302-9743 ; 4645
Keyword [en]
phylogenetic network, horizontal gene transfer, genome rearrangements, recombinations, minimum evolution
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-41116ISI: 000249739200010ScopusID: 2-s2.0-37249044190ISBN: 978-3-540-74125-1OAI: diva2:443638
7th International Workshop on Algorithms in Bioinformatics (WABI 2007) Location: Philadelphia, PA Date: SEP 08-09, 2007
Available from: 2011-09-26 Created: 2011-09-23 Last updated: 2011-09-26Bibliographically approved

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