Treelength Optimization for Phylogeny Estimation
We report missing branch rates for BeeTLe-Affine in comparison to ML methods, SATé, and SATé-II (top chart) and in comparison to MP methods (middle chart). On model conditions marked with ‘*’, ML(MAFFT)'s missing branch rate significantly improved upon BeeTLe-Affine's (using one-tailed pairwise t-tests with Benjamini-Hochberg  correction for multiple tests, for each test, and ). On model conditions marked with ‘$’, BeeTLe-Affine's missing branch rate significantly improved upon MP(MAFFT)'s (using similar statistical tests). Averages and standard error bars are shown; for each reported value.