Rogue

CRANRogueMaRDI QIDQ60638FDOQ60638

Identify Rogue Taxa in Sets of Phylogenetic Trees

Martin R. Smith, Andre J. Aberer

Last update: 29 November 2023

Copyright license: GNU General Public License

Software version identifier: 2.1.5, 1.0.0, 2.0.0, 2.1.0, 2.1.1, 2.1.2, 2.1.3, 2.1.4, 2.1.6

Description

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>.

Cites work

• Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees
• Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

Cited In (1)

• TreeSearch

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