You have to estimate the number of observation for each of the presence band (1) and the absence band (0). for example if you have one marker with 16 (1) and 4 (0), then the allele frequency of 1 is 16/(16+4) and for 0 is 4/(16+4). the sum of both frequencies must be 1

You have to estimate the number of observation for each of the presence band (1) and the absence band (0). for example if you have one marker with 16 (1) and 4 (0), then the allele frequency of 1 is 16/(16+4) and for 0 is 4/(16+4). the sum of both frequencies must be 1

You can use GenAIeX. It's an Add-in for Excel and easy to implement.

Hi i am using GenAlex for SSR data but i am confuse how can i measure the rare allele frequency.

You can use ADZE software.