Transfer RNA (tRNA) and ribosomal RNA (rRNA) genes are essential for the translation of messenger RNA (mRNA) into proteins. Studying how these genes evolve within a bacterial genus can reveal core sets of tRNA/rRNA genes and how these trends affect codon usage. The following research builds upon a previous algorithm called BOPAL which utilized operon information to better infer orthologous genes. The following research modifies BOPAL to properly handle singleton genes, adds a second pass to utilize previously inferred ancestors, and simplifies the backtracking algorithm by introducing a triple-wise alignment with a neighboring genome. These changes have culminated in a higher level of accuracy for the inferred events and ancestors compared to BOPAL. In our analysis, we also applied BOPAL 2.0 to a complex dataset of Clostridium genomes. Our results have found higher average rates of duplications, deletions, transpositions and substitution events in Clostridium than Bacillus but fewer inversions.