Extended Data Fig. 4: Comparison of FBP and TBE using the HIV dataset and FastTree phylogeny.
From: Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
FBP and TBE supports are compared with respect to branch depth, and tree size (see main text and legends of Figs. 1, 2 for explanations). Three support cut-offs are used to select the branches: 50%, 70% and 90% (for example, 1,624 branches among the 9,144 in total have TBE > 70% and 1,031 have FBP > 70%). Results are for the most part similar to those observed with the mammal dataset. We see a major effect of depth on FBP supports: with the full dataset, less than 1% of the deep (p > 16) branches have FBP support larger than 70%, whereas this percentage is higher than 20% with TBE. The effect of tree size is less pronounced. The fraction of supported branches decreases when the tree size increases from 35 to 571 taxa, but is analogous between 571 and 9,147 taxa. Furthermore, the gap between FBP and TBE remains similar, probably owing to the very large number of cherries and small clades, for which TBE and FBP are nearly equivalent. Regarding the support cut-off, 70% again appears as a good compromise for TBE, though there is no way to evaluate the fraction of supported branches that is actually erroneous. The interpretability of TBE will be a major asset for choosing the support level depending on the phylogenetic question being addressed. Here, as recombinant sequences are inevitable, lower supports than with mammals are likely to be acceptable.
