title: phangorn: phylogenetic analysis in R.
abstract: CONCLUSIONS
  phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.
  
  
  BACKGROUND
  phangorn can be obtained through the CRAN homepage http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.
authors.affiliation: UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, Paris, France. klaus.kschliep@snv.jussieu.fr
authors.forename: Klaus Peter
authors.initials: KP
authors.lastname: Schliep
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012984:Software