@article{fdi:010068790,
  title = {{A}pex : phylogenetics with multiple genes},
  author = {{J}ombart, {T}. and {A}rcher, {F}. and {S}chliep, {K}. and {K}amvar, {Z}. and {H}arris, {R}. and {P}aradis, {E}mmanuel and {G}oudet, {J}. and {L}app, {H}.},
  editor = {},
  language = {{ENG}},
  abstract = {{G}enetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. {W}hile such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. {I}n such cases, different loci should, at least as a preliminary step, be examined and analysed separately. {T}he {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. {U}nfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. {I}n 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. {I}n this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.},
  keywords = {genetics ; package ; phylogenies ; {R} ; software},
  booktitle = {},
  journal = {{M}olecular {E}cology {R}esources},
  volume = {17},
  numero = {1},
  pages = {19--26},
  ISSN = {1755-098{X}},
  year = {2017},
  DOI = {10.1111/1755-0998.12567},
  URL = {https://www.documentation.ird.fr/hor/fdi:010068790},
}