Steps to replicate

Scripts to execute	Intended result
qsub setup.sh	Create the directories for all phasing methods in the analysis, and populate with MCcoal data
run scripts/PHASE/phasingmodify.sh	Use the algorithm PHASE to resolve phase of all the datasets in the PHASED directory
run scripts/random/randommodify.sh	Resolves phase randomly for all the datasets in the random directory
run runbpp.sh	Submits all bpp jobs to the cluster in groups of 10 sequential analyses. Run with argument --fast to run 250 locus jobs individually to save time
run scripts/resubmit/checkcomplete.py	Produces a text file notfound.txt which lists all datasets that for any reason did not complete the analysis
run scripts/resubmit/fix.py	If there are files listed in notfound.txt, this will resubmit the correct jobs. If checkcomplete still finds uncompleted analyses after fix.py they must be manually submitted