fastbaps

Fastbaps is a rapid and efficient solution to the genetic clustering challenge, particularly tailored for multilocus genotype data. This software implements an approximate fit to a Dirichlet process mixture model (DPM), enabling it to handle substantially larger datasets—ranging from 10 to 100 times—than those manageable by existing model-based clustering methods. A key demonstration of its capability is the analysis of an alignment comprising over 110,000 sequences of HIV-1 pol genes, showcasing its robustness and scalability.

Beyond mere clustering, Fastbaps offers a novel approach for partitioning existing hierarchies to maximize the DPM model's marginal likelihood. This feature allows for the splitting of phylogenetic trees into clades and subclades based on a population genomic model, offering a nuanced view of genetic relationships and variations.