How many bootstrap replicates are necessary

Abstract. Phylogenetic Bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on recon-structing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on the most popular, Maximum Likelihood (ML). Be-cause ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the quality of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1– 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this paper, we propose stopping criteria, that is, thresholds com-puted at runtime to determine when enough replicates have been gener