Also, there are many transporters among the odd colored genes. Another cool site is Robert L. Charlebois genome and bioinformatics site . While it is not always clear what the beautiful pictures mean, some of the available tools are obviously great. Using the genetic mosaicism program, one can easily search for genes that were imported from outside the lineage of the organism. It clearly shows many small regions of duplications.
Gene clusters finds neighboring genes that have the same order in two genomes.
Kind of the same as above, but you get a listing of the clusters and their putative identification. In prokaryotes many molecular phylogenies are in conflict with each other. The reason for this is horizontal gene transfer. Prokaryotes do not have sex, where whole genomes have a chance to recombine with one another, they rely on the transfer of smaller fragments.