apex: phylogenetics with multiple genes
File(s)
Published version
Author(s)
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.
Date Issued
2016-08-12
Date Acceptance
2016-07-06
Citation
Molecular Ecology Resources, 2016, 17 (1), pp.19-26
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.
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
Medical Research Council (MRC)
Grant Number
MR/K010174/1B
Subjects
Genetics
Phylogenies
R
Software
package
Publication Status
Published