FGTpartitioner: A rapid method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets

Abstract

Abstract Partitioning large (e.g. chromosomal) alignments into ancestry blocks is a common step in phylogenomic analyses. However, current solutions require complicated analytical assumptions, or are difficult to implement due to excessive runtimes and unintuitive documentation. Additionally, most methods require haplotype phasing, which is often intractable for non-model studies. Here, I present an efficient and rapid solution for partitioning large genome alignments into ancestry blocks, which better accommodates non-model diploid organisms in that phasing information is not required a priori. FGTpartitioner processes a full-chromosome alignment orders of magnitude faster than alternative solutions, while recovering identical results, both via algorithmic improvements and the use of native parallelization. FGTpartitioner provides a means for simple and rapid block delimitation in genome-wide datasets as a pretext for phylogenomic analysis. It thus widens the potential uses for researchers studying phylogenetic processes across large, non-model genomes. Complete code and documentation for FGTpartitioner are available as an open-source repository on GitHub: https://github.com/tkchafin/FGTpartitioner