The advancing pace of fungal genome sequencing necessitates the timely analysis of data as it becomes available. We have developed a pipeline of perl scripts that connects several standalone programs to perform phylogenomic analysis and produce robust phylogenetic trees without excessive user input. These analyses are useful for resolving deep node relationships and has shown that automated fungal phylogenomics is feasible. It also has the promise of elucidating deep evolutionary relationships not resolved in conventional analyses with more limited character sampling. Phylogenomically generated phylogenies provided a well supported framework whereby protein clusters identified in a MCL matrix were characterized. Overlaying phylogenetically informed clusters with GO predictions and experimental data provided new insights to the origin of biological functions and processes within this well supported structure.