Inferring models of rearrangements, recombinations, and horizontal transfers by the minimum evolution criterion

Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

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.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
PublisherSpringer Verlag
Pages111-123
Number of pages13
ISBN (Print)9783540741251
DOIs
StatePublished - 2007
Event7th International Workshop on Algorithms in Bioinformatics, WABI 2007 - PhiIadelphia, PA, United States
Duration: 8 Sep 20079 Sep 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4645 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference7th International Workshop on Algorithms in Bioinformatics, WABI 2007
Country/TerritoryUnited States
CityPhiIadelphia, PA
Period8/09/079/09/07

Keywords

  • Genome rearrangements
  • Horizontal gene transfer
  • Minimum evolution
  • Phylogenetic network
  • Recombinations

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