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apex: phylogenetics with multiple genes.

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Date
2017-01
Authors
Jombart, Thibaut
Archer, Frederick
Schliep, Klaus
Kamvar, Zhian
Harris, Rebecca
Paradis, Emmanuel
Goudet, Jérome
Lapp, Hilmar
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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.
Type
Journal article
Subject
r
genetics
package
phylogenies
software
Computational Biology
Genes
Genetic Variation
Molecular Biology
Phylogeny
Sequence Homology
Software
Permalink
https://hdl.handle.net/10161/16027
Published Version (Please cite this version)
10.1111/1755-0998.12567
Publication Info
Jombart, Thibaut; Archer, Frederick; Schliep, Klaus; Kamvar, Zhian; Harris, Rebecca; Paradis, Emmanuel; ... Lapp, Hilmar (2017). apex: phylogenetics with multiple genes. Mol Ecol Resour, 17(1). pp. 19-26. 10.1111/1755-0998.12567. Retrieved from https://hdl.handle.net/10161/16027.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Lapp

Hilmar Lapp

Dir, IT
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