PT  - JOURNAL ARTICLE
AU  - F. Lemoine
AU  - J.-B. Domelevo Entfellner
AU  - E. Wilkinson
AU  - T. De Oliveira
AU  - O. Gascuel
TI  - Boosting Felsenstein’s Phylogenetic Bootstrap
AID  - 10.1101/154542
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 154542
4099  - http://biorxiv.org/content/early/2017/06/23/154542.short
4100  - http://biorxiv.org/content/early/2017/06/23/154542.full
AB  - Felsenstein’s article describing the application of the bootstrap to evolutionary trees, is one of the most cited papers of all time. That statistical method, based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies with hundreds or thousands of taxa are becoming routine. In that framework, Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. We propose a revised version, in which the presence of inferred branches in replications is measured using a gradual “transfer” distance, as opposed to the original version using a binary presence/absence index. The resulting supports are higher, while not inducing falsely supported branches. Our method is applied to large simulation, mammal and HIV datasets, for which it reveals the phylogenetic signal, while Felsenstein’s bootstrap fails to do so.