How to build phylogenetic species trees with OMA.
Détails
Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_D8D72D90D99B
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
How to build phylogenetic species trees with OMA.
Périodique
F1000Research
ISSN
2046-1402 (Electronic)
ISSN-L
2046-1402
Statut éditorial
Publié
Date de publication
2020
Peer-reviewed
Oui
Volume
9
Pages
511
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Publication Status: epublish
Résumé
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.
Mots-clé
OMA, Orthologous Matrix, phylogenetics, phylogenomics, species tree
Pubmed
Open Access
Oui
Création de la notice
04/04/2023 16:08
Dernière modification de la notice
23/01/2024 8:35