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bioRxiv · 10.1101/2024.09.25.615070

Skeletons in the Forest: Using Entropy-Based Rogue Detection on Bayesian Phylogenetic Tree Distributions

Klawitter, J.·Bouckaert, R. R.·Drummond, A. J.
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Abstract

In a phylogenetic analysis, rogue taxa and clades are those that, due to their uncertain placement, contribute disproportionally to the variance in a set of phylogenetics trees. They can obscure clear evolutionary relationships and complicate the interpretation of results. While existing rogue detection algorithms focus on improving the consensus tree for a set of trees, we introduce algorithms based on phylogenetic entropy to improve the analysis in a Bayesian framework. In particular, we introduce a tool that extracts a skeleton distribution of the posterior tree distribution that contains the core relationships by removing a minimal subset of rogues. Additionally, we enable detailed analyses of rogues at both the taxon and clade levels, including the visualisation of different rogue placements.

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Klawitter, J., Bouckaert, R. R., Drummond, A. J.. 2024-09-27. Skeletons in the Forest: Using Entropy-Based Rogue Detection on Bayesian Phylogenetic Tree Distributions. https://doi.org/10.1101/2024.09.25.615070

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