apex: phylogenetics with multiple genes

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Title: apex: phylogenetics with multiple genes
Author(s): Jombart, T
Archer, F
Schliep, K
Kamvar, Z
Harris, R
Paradis, E
Goudet, J
Lapp, H
Item Type: Journal Article
Abstract: Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria, and Eucaryotes. 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 paper, 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 analyzing these data. In this paper, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple dataset. This article is protected by copyright. All rights reserved.
Publication Date: 12-Aug-2016
Date of Acceptance: 6-Jul-2016
URI: http://hdl.handle.net/10044/1/38458
DOI: https://dx.doi.org/10.1111/1755-0998.12567
ISSN: 1755-0998
Publisher: Wiley
Start Page: 19
End Page: 26
Journal / Book Title: Molecular Ecology Resources
Volume: 17
Issue: 1
Copyright Statement: © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Sponsor/Funder: Medical Research Council (MRC)
Funder's Grant Number: MR/K010174/1B
Keywords: Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Ecology
Evolutionary Biology
Environmental Sciences & Ecology
genetics
package
phylogenies
R
software
MULTIVARIATE-ANALYSIS
R-PACKAGE
TOOLS
INCONGRUENCE
POPULATIONS
TECHNOLOGIES
EVOLUTION
MARKERS
TREES
r
genetics
package
phylogenies
software
Computational Biology
Genes
Genetic Variation
Molecular Biology
Phylogeny
Sequence Homology
Software
Computational Biology
Molecular Biology
Phylogeny
Sequence Homology
Genes
Software
Genetic Variation
Genetics
Phylogenies
R
Software
package
06 Biological Sciences
Evolutionary Biology
Publication Status: Published
Appears in Collections:Faculty of Medicine
Epidemiology, Public Health and Primary Care



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