Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments

A bstract Many phylogenomic studies used non-overlapping windows to address gene tree discordance across a set of aligned genomes. Recently, Ivan et al. (2025) proposed an information theoretic approach to choose an optimal window size given the alignment. However, this approach selects only a single fixed window size per chromosome, which is a useful first step but fails to account for variation in the size of non-recombining regions along each chromosome. In this study, we extend the approach of Ivan et al. (2025) and propose PhyloNOW (phylogenomic non-overlapping windows) that allows window sizes to vary across the chromosome. We show that PhyloNOW outperforms the fixed-size approach on a wide range of simulated datasets. Applying the new method on two empirical datasets from Heliconius butterflies and great apes, we show that window sizes vary substantially across chromosomes. Our study highlights the limitations of using a fixed window size in non-overlapping window analyses, and proposes PhyloNOW that allows for variable window sizes across whole genome alignments. PhyloNOW is available at https://github.com/jeremiasivan/PhyloNOW .