Manuscript release

This release is coming many years after the fact but co-incides with the release of the manuscript: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005184

Which is to say, the code contained in this release was used in the aforementioned manuscript. Some changes may occur in the future to address community needs and these changes may/may not be as comprehensively error tested.