Running time on 100-taxon non-ILS datasets Average running time (y-axis given in log-scale) of methods on 100-taxon non-ILS datasets with MAFFT alignments of (A) 25 and (B) 50 genes. MrBayes performed two runs of 1M MCMC iterations in each analysis, with an average running time of 25 hours per sequence alignment. At the end of its analysis, MrBayes reported an average standard deviation of bipartitions at 0.065, indicating that it was far from convergence. BUCKy used 15K trees per gene for the full MrBayes distribution and 2K trees per gene on the sparse. RAxML performed 100 bootstrap replicates under GTRCAT. BUCKy analyses on RAxML used 100 trees per gene.