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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2.0.0 by Martin R. Smith, 3 months ago,,

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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