• Branch code
• Remove extraneous files
• Move src to top level

Ensure that PH-007,008,009,010 all make it in with their 16-23S regions.

• Single Isolate, all params, one algorithm
• Single Isolate, all params, all algorithms
• All Isolates, one param set, one algorithm
• All Isolates, one param set, all algorithms

Currently, you have the precision for a species -- how many times are chickens accurately classified as chickens. Instead, look when something is classified as a chicken, how many times that is actually a chicken.

This will affect a few classes here. Start with the Pyroprint class and add the flag. Then Parse it using the TreeBuilder. There may be more it affects, look at the hierarchy.

Don't compare pyroprints if they're from the same isolate and see how that affects the data. Consider doing a small comparison study so we understand the differences. You should see differences in Bats, hopefully. Apparently there are only a couple of Isolates there.

• Move it to Maven
• Rewrite Driver options to use a canned library
• Figure out how to incorporate Python scripts appropriately
• Write documentation
• Consider making multiple drivers

• Write Prequisites
  • Explain how to setup MySQL?
• Write Usage
  • Pull from Makefile
• Email Tram