Imperial College London
Alternate

DrThibautJombart

Faculty of Medicine, School of Public Health

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 3658t.jombart Website

 
 
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Location

 

UG11Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Jombart:2016:10.1111/1755-0998.12567,
author = {Jombart, T and Archer, F and Schliep, K and Kamvar, Z and Harris, R and Paradis, E and Goudet, J and Lapp, H},
doi = {10.1111/1755-0998.12567},
journal = {Molecular Ecology Resources},
pages = {19--26},
title = {apex: phylogenetics with multiple genes},
url = {http://dx.doi.org/10.1111/1755-0998.12567},
volume = {17},
year = {2016}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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.
AU  - Jombart,T
AU  - Archer,F
AU  - Schliep,K
AU  - Kamvar,Z
AU  - Harris,R
AU  - Paradis,E
AU  - Goudet,J
AU  - Lapp,H
DO  - 10.1111/1755-0998.12567
EP  - 26
PY  - 2016///
SN  - 1755-0998
SP  - 19
TI  - apex: phylogenetics with multiple genes
T2  - Molecular Ecology Resources
UR  - http://dx.doi.org/10.1111/1755-0998.12567
UR  - http://hdl.handle.net/10044/1/38458
VL  - 17
ER  -
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