ML formulation seems to be working at a basic level
Changed encoding of flip state from (bool,bool) to an enum.  Committing to recover probabilistic code if it turns out to be useful.
Major Commit: ISMB version of code.  Still needs to be greatly cleaned up and optimized, but it should be functionally complete
initial ISMB version
commit for upload to Lane center machine
commit for upload to Lane center machine
fixed case issue
removed some unnecessary tests, speed improvement
added support for cross-validation input files
Massive update to CMakeLists.txt to pull in all external dependencies apart from Boost.  Other updates to main code.
Working commit pre-species synchronization
Inching toward initial release