Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.

Package details

AuthorMartin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Andre J. Aberer [aut, cph]
MaintainerMartin R. Smith <martin.smith@durham.ac.uk>
LicenseGPL (>= 3)
Version2.1.0
URL https://github.com/ms609/Rogue/ https://github.com/aberer/RogueNaRok/ https://github.com/ms609/RogueNaRok/
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("Rogue")

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Rogue documentation built on Jan. 13, 2022, 5:07 p.m.