PhyloBayes is a software program for Bayesian phylogenetic reconstruction. Compared to other programs, its main distinguishing feature is the implementation of the CAT model, which accounts for fine-grained variation across sites in amino acid preferences using a Bayesian non-parametric approach. This chapter provides a detailed step-by-step practical introduction to phylogenetic analyses using PhyloBayes, using as an example a previously published dataset addressing the phylogenetic position of Microsporidia within eukaryotes. Through this historically emblematic case of a long-branch attraction artifact, a complete analysis under site-homogeneous and site-heterogeneous models is conducted and interpreted, thus providing an illustration of why modeling pattern variation is so fundamental for reconstructing deep phylogenies.