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How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved with reservations]

Dylus, David; Nevers, Yannis; Altenhoff, Adrian M; Gürtler, Antoine; Dessimoz, Christophe; Glover, Natasha M; (2022) How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved with reservations]. F1000Research , 9 , Article 511. 10.12688/f1000research.23790.2. Green open access

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Abstract

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.

Type: Article
Title: How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved with reservations]
Open access status: An open access version is available from UCL Discovery
DOI: 10.12688/f1000research.23790.2
Publisher version: https://doi.org/10.12688/f1000research.23790.2
Language: English
Additional information: © 2022 Dylus D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Phylogenetics, phylogenomics, species tree, OMA, Orthologous Matrix
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10144891
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