title: ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.
abstract: Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions.
  
  
  BACKGROUND
  ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/web/packages/ape/index.html Further information may be found at http://ape.mpl.ird.fr/pegas/
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
authors.forename: Andrei-Alin
authors.initials: AA
authors.lastname: Popescu
authors.forename: Katharina T
authors.initials: KT
authors.lastname: Huber
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Paradis
mesh_terms: D005075:Biological Evolution; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software