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, forthcoming), and an interface to 'RogueNaRok' (Aberer et al. 2013) .


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install.packages("Rogue")

2.0.0 by Martin R. Smith, a month ago


https://github.com/ms609/Rogue/, https://github.com/aberer/RogueNaRok/, https://github.com/ms609/RogueNaRok/


Report a bug at https://github.com/ms609/Rogue/issues/


Browse source code at https://github.com/cran/Rogue


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


Documentation:   PDF Manual  


GPL (>= 3) license


Imports ape, cli, fastmatch, grDevices, matrixStats, Rdpack, Rfast, stats, TreeDist, TreeTools, utils

Suggests testthat

System requirements: C99


Imported by TreeSearch.


See at CRAN