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Titel: Phylogenetics from paralogs
Verfasser: Hellmuth, Marc
Wieseke, Nicolas
Lechner, Markus
Lenhof, Hans-Peter
Middendorf, Martin
Stadler, Peter F.
Sprache: Englisch
Erscheinungsjahr: 2014
SWD-Schlagwörter: Bioinformatik
Genetik
Freie Schlagwörter: phylogeny
paralogs
cograph
rooted triples
integer linear program
NP-complete
DDC-Sachgruppe: 004 Informatik
Dokumentart : Journalartikel
Kurzfassung: Motivation: Sequence-based phylogenetic approaches heavily rely on initial data sets to be composed of orthologous sequences only. Paralogs are treated as a dangerous nuisance that has to be detected and removed. Recent advances in mathematical phylogenetics, however, have indicated that gene duplications can also convey meaningful phylogenetic information provided orthologs and paralogs can be distinguished with a degree of certainty. Results: We demonstrate that plausible phylogenetic trees can be inferred from paralogy information only. To this end, tree-free estimates of orthology, the complement of paralogy, are first corrected to conform cographs and then translated into equivalent event-labeled gene phylogenies. A certain subset of the triples displayed by these trees translates into constraints on the species trees. While the resolution is very poor for individual gene families, we observe that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees of several groups of eubacteria. The novel method introduced here relies on solving three intertwined NP-hard optimization problems: the cograph editing problem, the maximum consistent triple set problem, and the least resolved tree problem. Implemented as Integer Linear Program, paralogy-based phylogenies can be computed exactly for up to some twenty species and their complete protein complements. Availability:The ILP formulation is implemented in the Software ParaPhylo using IBM ILOG CPLEX (TM) Optimizer 12.6 and is freely available from http://pacosy.informatik.uni-leipzig.de/paraphylo
Link zu diesem Datensatz: urn:nbn:de:bsz:291-scidok-57969
hdl:20.500.11880/26621
http://dx.doi.org/10.22028/D291-26565
SciDok-Publikation: 27-Mai-2014
Fakultät: Fakultät 6 - Naturwissenschaftlich-Technische Fakultät I
Fachrichtung: MI - Informatik
Fakultät / Institution:MI - Fakultät für Mathematik und Informatik

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