Extended Data Fig. 2: Comparison of FBP and TBE using the mammal 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, quartet conflicts with the NCBI taxonomy 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, 28 branches among the 1,446 in total have TBE ≥ 90% and 11 have FBP ≥ 90%). The FastTree topology is poor, with 38% of quartets contradicted by the NCBI taxonomy, and 404 of the 1,441 branches with contradictions above 20%. Despite this difficulty, FBP and TBE perform well: they give supports larger than 70% to a very low number of moderately ((5,20]%) and highly (> 20%) conflictual branches. FBP supports very few deep branches, whereas TBE supports a larger number of branches and is especially useful with large trees. Comparing the three cut-offs, we see that with a 50% cut-off the selected branches are still weakly contradicted, especially with FBP; as expected, with TBE the fraction of contradicted branches (> 5%) is a bit higher but still low (∼7%). With a cut-off of 90% very few branches are selected (∼2% with TBE), thus justifying the use of the 70% threshold for TBE—as is standard with FBP.
