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apex : phylogenetics with multiple genes
Author(s) -
Jombart Thibaut,
Archer Frederick,
Schliep Klaus,
Kamvar Zhian,
Harris Rebecca,
Paradis Emmanuel,
Goudet Jérome,
Lapp Hilmar
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12567
Subject(s) - phylogenetic tree , biology , phylogenetics , phylogenetic network , set (abstract data type) , limiting , r package , evolutionary biology , computational biology , gene , genetics , computer science , mechanical engineering , computational science , engineering , programming language
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.