@article{PAR00008930,
  title = {{A}pe 3.0 : new tools for distance-based phylogenetics and evolutionary analysis in {R}},
  author = {{P}opescu, {A}. {A}. and {H}uber, {K}. {T}. and {P}aradis, {E}mmanuel},
  editor = {},
  language = {{ENG}},
  abstract = {{R}eflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. {A}mong 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. {H}owever, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. {O}ne 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). {S}o far their analysis has been out of reach for ape. {T}o remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. {I}n 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.},
  keywords = {},
  booktitle = {},
  journal = {{B}ioinformatics},
  volume = {28},
  numero = {11},
  pages = {1536--1537},
  ISSN = {1367-4803},
  year = {2012},
  DOI = {10.1093/bioinformatics/bts184},
  URL = {https://www.documentation.ird.fr/hor/{PAR}00008930},
}