Added some new directories to scripts folder. TDM
Committing many changes. Haven't done it in a long time. Oops. TDM 1/9/14
Made changes to BetweenGenomeSpatialBias.py to do proportion shared instead of number of events. Changed RecombinationProgramPlot.R to also plot ClonalOrigin results. Changed ProgramAccuracy.py to use a .9 posterior probability threshold for ClonalFrame or ClonalOrigin. Updated ParseClonalOrigin.py. TDM
Moved files into new directory called Misc
Merged with testing branch
Added BetweenGenomeSpatialBiasAnalysis to the repository
Added 75% shared calculation
Added RemoveRecombinantRegions.py to the repository
Added function to remove recombinant regions of alignment
outputs null distribution to a file now
Added scripts to calculate p-values for spatial bias
Edited scripts to correctly output null distribution
Merge branch 'master' of https://github.com/tatumdmortimer/recombination