The fungal research community has enjoyed an explosion of new data due to the rapid advancement of sequencing technology.  The increase in the production of genomic data now makes it feasible to sequence the genomes of organisms from the same genus for use as synergistic analysis tools.  To that end the Department of Energy Joint Genome Institute has recently sequenced the genomes of two other species from the genus Trichoderma, T. virens and T. atroviride, to assist in the understanding of the well known biomass degrading fungus Trichoderma reesei.  We performed several analyses to basis our comparative analysis on.  To understand how genomes evolve we first calculated synteny (greek for same ribbon) using the maximum gap cluster method.  As expected, we discovered a high amount of conserved synteny between the three organisms, with notable exceptions.  We next calculated the rate of non-synonymous (K_a) to the rate of synonymous substitutions (K_s) between orthologs (genes from each organism that were the same in the most recent common ancestor) of all three organisms to identify genes that are under positive selection.  Next we calculated paralogs (genes that have duplicated since the most recent common ancestor) in an attempt to understand why T. reesei has 9129 genes, and T. virens and T. atroviride contain more than 11,000 each. Finally, as we found clusters of important biomass degrading enzymes in T. reesei, we discovered similar clusters in T. virens and T. atroviride.