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] (<>), Andre J. Aberer [aut, cph]
MaintainerMartin R. Smith <>
LicenseGPL (>= 3)
Package repositoryView on CRAN
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Rogue documentation built on Jan. 13, 2022, 5:07 p.m.