apex: phylogenetics with multiple genes.

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Version: Final published version
Serval ID
serval:BIB_7D5430D54AEB
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
apex: phylogenetics with multiple genes.
Journal
Molecular Ecology Resources
Author(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
Publication state
Published
Issued date
2017
Peer-reviewed
Oui
Volume
17
Number
1
Pages
19-26
Language
english
Abstract
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.
Keywords
Computational Biology/methods, Genes, Genetic Variation, Molecular Biology/methods, Phylogeny, Sequence Homology, Software, r, genetics, package, phylogenies, software
Pubmed
Web of science
Open Access
Yes
Create date
12/01/2017 15:10
Last modification date
20/08/2019 15:38
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