apex : phylogenetics with multiple genes - Université de Montpellier Accéder directement au contenu
Article Dans Une Revue Molecular Ecology Resources Année : 2017

apex : phylogenetics with multiple genes

Thibaut Jombart
  • Fonction : Auteur
  • PersonId : 926089
Frederick Archer
  • Fonction : Auteur
Klaus Schliep
  • Fonction : Auteur
Zhian Kamvar
  • Fonction : Auteur
Rebecca Harris

Résumé

Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The R software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new R package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.
Fichier principal
Vignette du fichier
apex phylogenetics with multiple genes.pdf (699.13 Ko) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

hal-01821911 , version 1 (16-12-2020)

Licence

Paternité

Identifiants

Citer

Thibaut Jombart, Frederick Archer, Klaus Schliep, Zhian Kamvar, Rebecca Harris, et al.. apex : phylogenetics with multiple genes. Molecular Ecology Resources, 2017, 17 (1), pp.19 - 26. ⟨10.1111/1755-0998.12567⟩. ⟨hal-01821911⟩
173 Consultations
65 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More