I need to analysis my agarose gels. I am trying out a few methods using RFLP and restriction enzymes that will bring out more variation in my samples, and I have been asked to analysis my results by scoring for present (1) or absence (0) of bands for all my samples. I can't seem to find a step by step guide on how to perform this analysis and wanted to get some guide on performing this binary scoring on my gels. Any guide or help will be much appreciated.

There is software that can analyse and quantify bands, it is often part of the gel dock photo software that takes the picture in the first place. Presence/absence can be empirically determined by looking at a background segment (ie no band) and defining a band as some minimum brightness above background.

It can also be acceptable to assess by eye. If this were me, I would look for a discrete band at the right size and try convince myself that it is not a gel artifact through smearing or just random staining inconsistancies. I may need to run the same sample twice, or load more on to the gel to be sure.

Having said all that, you really need to speak to your supervisor/boss or other senior members of your group to nail this technique down properly.