Extended Data Fig. 3: Comparison of FBP and TBE using the mammal dataset and the phylogeny inferred by RAxML with rapid bootstrap.
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, 41 branches among the 1,446 in total have TBE ≥ 90% and 19 have FBP ≥ 90%). The RAxML topology is closer to the NCBI taxonomy than is the FastTree topology (27% versus 38% of contradicted quartets, and 353 versus 404 branches with contradiction > 20%, respectively). However, the RAxML topology is still relatively poor, as expected in this type of phylogenetic study based on a unique marker (Fig. 4 and main text). Despite this difficulty, FBP and TBE perform well as they give supports larger than 70% to a very low number of moderately ((5,20]%) and highly (> 20%) conflictual branches. The supports obtained with RAxML are higher than those obtained with FastTree (47 versus 29 branches with FBP > 70% for RAxML and FastTree, respectively; 158 versus 108 branches with TBE > 70% for RAxML and FastTree, respectively). Part of the explanation could be that the RAxML tree is more accurate than that of FastTree, and is thus better supported. Another factor is that the rapid bootstrap tends to be more supportive than the standard procedure, as shown in previous publications16. Indeed, the rapid bootstrap uses already inferred trees to initiate tree searching, and therefore tends to produce less diverse bootstrap trees than the standard, slower procedure, which restarts tree searching from the very beginning for each replicate. Despite these differences between FastTree and RAxML with rapid bootstrap, similar conclusions are drawn when comparing FBP and TBE: FBP supports very few deep branches, whereas TBE supports a larger number of them; TBE is especially useful with large trees; and both methods support a very low number of contradicted branches. Comparing the support cut-offs, 70% again appears as a good compromise for both FBP and TBE.
