apex: phylogenetics with multiple genes.

Détails

Ressource 1Télécharger: 27417145_BIB_7D5430D54AEB.pdf (708.69 [Ko])
Etat: Serval
Version: Final published version
ID Serval
serval:BIB_7D5430D54AEB
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
apex: phylogenetics with multiple genes.
Périodique
Molecular Ecology Resources
Auteur(s)
Jombart T., Archer F., Schliep K., Kamvar Z., Harris R., Paradis E., Goudet J., Lapp H.
ISSN
1755-0998 (Electronic)
ISSN-L
1755-098X
Statut éditorial
Publié
Date de publication
2017
Peer-reviewed
Oui
Volume
17
Numéro
1
Pages
19-26
Langue
anglais
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.
Mots-clé
Computational Biology/methods, Genes, Genetic Variation, Molecular Biology/methods, Phylogeny, Sequence Homology, Software, r, genetics, package, phylogenies, software
Pubmed
Web of science
Open Access
Oui
Création de la notice
12/01/2017 15:10
Dernière modification de la notice
08/05/2019 20:56
Données d'usage