Added top directories
Populated svn trunk
Moved run simulation command line script to Utils as entry point.
Added some help text and command line parsing
Fixed a namespace issue
Added specification of a bppseqgen options file
Added a bppseqgen options file
Added functionality to allow the branch where recombinations occur to be identified. Added functions for running the ILS CTMC.
Added functionality to allow the branch where recombinations occur to be identified. Added functions for running the ILS CTMC.
Added entry point for ctmc ILS script
Added runCTMC.py for running the ILC CTMC
Merge https://github.com/kaspermunch/SimulationPipeline