Many other programs have been written but their application is very specialised to the project and I haven't included them here, as they probably won't be much use to anyone else. If you are interested however please email me at e.ryder[at]gen.cam.ac.uk
All of these programs are perl scripts and require linux / unix with perl installed to run.
Many of the programs require .sqo files, which are the genome sequence in one contiguous chunk per chromosome. These can be downloaded here. Warning - the zip file is over 30megs in size, and expands to over 120megs.