Quick start guide and overview

The following figure (which is also part of the supplemental material for the ITEP manuscript) provides a concise overview of the organization of data within the framework and directions on how to quickly get started with the ITEP analysis (note that by quickly I mean human time - running BLAST all vs. all, RPSBLAST, and MCL can all take significant amounts of computer time). $root refers to the root directory of your ITEP repository.