TY - JOUR T1 - Fast Hierarchical Bayesian Analysis of Population Structure JF - bioRxiv DO - 10.1101/454355 SP - 454355 AU - Gerry Tonkin-Hill AU - John A. Lees AU - Stephen D. Bentley AU - Simon D.W. Frost AU - Jukka Corander Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/10/26/454355.abstract N2 - We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly identifies an approximate fit to a Dirichlet Process Mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach is able to cluster datasets 10-100 times larger than the existing model-based methods, which we demonstrate by analysing an alignment of over 110,000 sequences of HIV-1 pol genes. We also provide a method for rapidly partitioning an existing hierarchy in order to maximise the DPM model marginal likelihood, allowing us to split phylogenetic trees into clades and subclades using a population genomic model. Extensive tests on simulated data as well as a diverse set of real bacterial and viral datasets show that fastbaps provides comparable or improved solutions to previous model-based methods, while generally being significantly faster. The method is made freely available under an open source MIT licence as an easy to use R package at https://github.com/gtonkinhill/fastbaps. ER -