TY - GEN
T1 - Inferring models of rearrangements, recombinations, and horizontal transfers by the minimum evolution criterion
AU - Birin, Hadas
AU - Gal-Or, Zohar
AU - Elias, Isaac
AU - Tuller, Tamir
PY - 2007
Y1 - 2007
N2 - 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.
AB - 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.
KW - Genome rearrangements
KW - Horizontal gene transfer
KW - Minimum evolution
KW - Phylogenetic network
KW - Recombinations
UR - http://www.scopus.com/inward/record.url?scp=37249044190&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-74126-8_11
DO - 10.1007/978-3-540-74126-8_11
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AN - SCOPUS:37249044190
SN - 9783540741251
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 111
EP - 123
BT - Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
PB - Springer Verlag
T2 - 7th International Workshop on Algorithms in Bioinformatics, WABI 2007
Y2 - 8 September 2007 through 9 September 2007
ER -