philr

The software tool PhILR introduces the PhILR transform, integrating microbial evolutionary models with the isometric log-ratio transform to address statistical artifacts commonly encountered in analyzing relative abundance data from microbial community surveys. This transformation enables the application of standard statistical tools to microbiota surveys, providing results comparable to or superior to conventional methods when assessing community-level structure. Additionally, the PhILR transform facilitates the identification of neighboring clades adapted to distinct human body sites by decomposing distance in transformed space. The variance decomposition analysis highlights increased covariation of bacterial clades within human body sites with phylogenetic relatedness.