title: Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion.
abstract: BACKGROUND
  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 materials (HGTS). 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. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input.
  
  
  RESULTS
  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. We 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 four biological datasets.
  
  
  BACKGROUND
  The code is available from the authors upon request.
authors.affiliation: School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Hadas
authors.initials: H
authors.lastname: Birin
authors.forename: Zohar
authors.initials: Z
authors.lastname: Gal-Or
authors.forename: Isaac
authors.initials: I
authors.lastname: Elias
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods; D019143:Evolution, Molecular; D015329:Gene Rearrangement, T-Lymphocyte / Q000235:genetics*; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D010940:Plant Proteins