How to build phylogenetic species trees with OMA.

Autor:	Dylus D; Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.; Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland., Nevers Y; Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.; Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland., Altenhoff AM; Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.; Department of Computer Science, ETH Zurich, Zurich, 8092, Switzerland., Gürtler A; Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.; Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland., Dessimoz C; Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.; Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.; Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.; Department of Computer Science, University College London, London, WC1E 6BT, UK., Glover NM; Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.; Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
Jazyk:	angličtina
Zdroj:	F1000Research [F1000Res] 2020 Jun 04; Vol. 9, pp. 511. Date of Electronic Publication: 2020 Jun 04 (Print Publication: 2020).
DOI:	10.12688/f1000research.23790.1
Abstrakt:	Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done ad hoc . This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples. Competing Interests: No competing interests were disclosed. (Copyright: © 2020 Dylus D et al.)
Databáze:	MEDLINE
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