title: apex: phylogenetics with multiple genes.
abstract: 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.
authors.affiliation: Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
authors.forename: Thibaut
authors.identifier: http://orcid.org/0000-0003-2226-8692
authors.initials: T
authors.lastname: Jombart
authors.affiliation: Southwest Fisheries Science Center, NMFS-NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037-1508, USA.
authors.forename: Frederick
authors.initials: F
authors.lastname: Archer
authors.affiliation: Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125-3393, USA.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schliep
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, 2701 SW Campus Way, Corvallis, OR, 97331, USA.
authors.forename: Zhian
authors.initials: Z
authors.lastname: Kamvar
authors.affiliation: Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195-1800, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Harris
authors.affiliation: Institut des Sciences de l'Évolution, Université Montpellier - CNRS - IRD - EPHE, Place Eugène Bataillon - CC 065, 34095, Montpellier cédex 05, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Paradis
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Le Biophore CH - 1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, University of Lausanne, Quartier Sorge - Batiment Genopode 1015, Lausanne, Switzerland.
authors.forename: Jérome
authors.initials: J
authors.lastname: Goudet
authors.affiliation: Duke Center for Genomic and Computational Biology (GCB), Duke University CIEMAS, 101 Science Drive, DUMC Box 3382, Durham, NC, 27708, USA.
authors.forename: Hilmar
authors.initials: H
authors.lastname: Lapp
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005796:Genes; D014644:Genetic Variation; D008967:Molecular Biology / Q000379:methods*; D010802:Phylogeny; D017385:Sequence Homology; D012984:Software
keywords: 
  r
  ; genetics; package; phylogenies; software