Package: Rogue 2.2.1.9000

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 tips. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>, and heuristics for measuring leaf instability.

Authors:Martin R. Smith [aut, cre, cph], Andre J. Aberer [aut, cph]