Hi there too
The problem is not whether the bands are faint, but if they are reproducible!
So always run replicate reactions so there can be no mistake about fragments.
If the fragments are too faint, try incorporating biotin (dUTP) during the last ten rounds od amplification. Visualisation after blotting of the pattern with
AMPPD (chemoluminiscence kits are available from many sources) will confirm
the faintest fragments. If fragments are reproducible, yes they should be scored.
As for differences within and between populations, it is best to try to
identify "signature fragments" for each population. Ideally these are fragments present as a monomorphic band in one population and absent in any other.
Another, more basic problem seems to be: how is a RAPD locus defined?
Is it just the stretch of DNA between two primer sites, is it just one primer site, both primer sites? Only when a good definition of a RAPD locus is available
there is a possibility of meaningful quantitative comparison of species.
You can subscribe to a RAPD newsgroup by sending the command
subscribe RAPD-L <your name> to listserv at buyvm
I have not yet heard of any computer programs for RAPD data, possibly due to the above described troublesome interpretation of RAPD loci.
Good luck with your data-set.
Louis v.d. Zande