TY - JOUR
T1 - apex
T2 - phylogenetics with multiple genes
AU - Jombart, Thibaut
AU - Archer, Frederick
AU - Schliep, Klaus
AU - Kamvar, Zhian
AU - Harris, Rebecca
AU - Paradis, Emmanuel
AU - Goudet, Jérome
AU - Lapp, Hilmar
PY - 2017/1
Y1 - 2017/1
N2 - 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.
AB - 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.
KW - Computational Biology/methods
KW - Genes
KW - Genetic Variation
KW - Molecular Biology/methods
KW - Phylogeny
KW - Sequence Homology
KW - Software
U2 - 10.1111/1755-0998.12567
DO - 10.1111/1755-0998.12567
M3 - Article
C2 - 27417145
SN - 1755-098X
VL - 17
SP - 19
EP - 26
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 1
ER -