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GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss

Morel, B.; Kozlov, A. M.; Stamatakis, Alexandros 1; Szöllősi, G. J.
1 Institut für Theoretische Informatik (ITI), Karlsruher Institut für Technologie (KIT)


Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges, species-tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data preprocessing (e.g., computing bootstrap trees) and rely on approximations and heuristics that limit the degree of tree space exploration. Here, we present GeneRax, the first maximum likelihood species-tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. ... mehr

Verlagsausgabe §
DOI: 10.5445/IR/1000125218
Veröffentlicht am 23.10.2020
DOI: 10.1093/molbev/msaa141
Zitationen: 48
Web of Science
Zitationen: 41
Zitationen: 83
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2020
Sprache Englisch
Identifikator ISSN: 0737-4038, 1537-1719
KITopen-ID: 1000125218
Erschienen in Molecular biology and evolution
Verlag Oxford University Press (OUP)
Band 37
Heft 9
Seiten 2763-2774
Vorab online veröffentlicht am 05.07.2020
Schlagwörter gene family tree, reconciliation, maximum likelihood, gene duplication, horizontal gene transfer
Nachgewiesen in Dimensions
Web of Science
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