I'm working on genetic diversity of Groundnut/Peanut. For that I have to use SSRs. I just want to know which dye is best. My amplified allele size is approx 200bp.
In India most of the sequencing instruments are dye sensitive for fragment analysis. The most commonly used M13 dyes for fragment analysis are 6FAM, VIC, NED, PET, TET, HEX. (6-FAM is a non-proprietary dye and all others are proprietary dyes).
Some times dyes are specific to primers. As in your case the product size was around 200bp so I think 6FAM or VIC or HEX will be suitable..
for the first, check for which dyes the equipment that you would like to use has done a spectral calibration.
for the second, you have to choose pair of dyes which could be analysed in one run (capillary). Your sample will have one and a size standard the second one.