title: treespace: Statistical exploration of landscapes of phylogenetic trees.
abstract: The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results.
authors.affiliation: Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, UK.
authors.forename: Thibaut
authors.identifier: http://orcid.org/0000-0003-2226-8692
authors.initials: T
authors.lastname: Jombart
authors.affiliation: Department of Mathematics, Imperial College London, London, UK.
authors.forename: Michelle
authors.initials: M
authors.lastname: Kendall
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Jacob
authors.initials: J
authors.lastname: Almagro-Garcia
authors.affiliation: Department of Mathematics, Imperial College London, London, UK.
authors.forename: Caroline
authors.initials: C
authors.lastname: Colijn
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D010802:Phylogeny; D012984:Software; D014197:Trees / Q000145:classification* / Q000235:genetics*
keywords: incongruence; multivariate analysis; package; software; tree distances; tree metric