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treespace : Statistical exploration of landscapes of phylogenetic trees
Author(s) -
Jombart Thibaut,
Kendall Michelle,
AlmagroGarcia Jacob,
Colijn Caroline
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12676
Subject(s) - phylogenetic tree , phylogenetics , biology , computational phylogenetics , phylogenetic network , tree (set theory) , tree of life (biology) , evolutionary biology , tree rearrangement , multivariate statistics , toolbox , bayesian probability , phylogenetic comparative methods , computational biology , machine learning , computer science , artificial intelligence , genetics , mathematics , gene , mathematical analysis , programming language
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.