2012-11-2 Andrew J. Page <ap13@sanger.ac.uk>
* Prefilters the initial alignment, ignoring sequences with >25% missing data (the '--filter_percentage' parameter lets you vary this).  
* SNPs are outputted on a per branch basis in tab format.
* The stats are now on a per branch basis rather than cumulatively built up from walking the tree.
* Node labelling in the recombination tab file now consistent with the tree internal node labels

2012-8-7 Andrew J. Page <ap13@sanger.ac.uk>
* Cleanup intermediate files by default
* Fix RF distance calculation and comparison

2012-4-24 Andrew J. Page <ap13@sanger.ac.uk>
* Initial beta testing version