Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.

ABSTRACT: Gene tree discordance along a set of aligned genomes presents a challenge for phylogenomic methods to identify the non-recombining regions and reconstruct the phylogenetic tree for each region. To address this problem, many studies used the non-overlapping window approach, often with an arbitrary selection of fixed window sizes that potentially include intra-window recombination events. In this study, we propose an information theoretic approach to select a window size that best reflects the underlying histories of the alignment. First, we simulated chromosome alignments that reflected the key characteristics of an empirical data set and found that the Akaike information criterion (AIC) is a good predictor of window size accuracy in correctly recovering the tree topologies of the alignment

SUBMITTER: Ivan J 

PROVIDER: S-EPMC12805665 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature