Does anyone use DNAsp for calculating nucleotide or gene diversity? I love how easy it is to use - but I have a question about formatting data for these two calculations.
In Arlequin you need each unique haplotype on a line designated with 1) sample ID and 2) number of individuals with that haplotype
In DNAsp I haven't figured out a way to denote the number of individuals with each particular haplotype - is there a way of doing this either in the .meg file or within DNAsp once the data is imported? Alternately - can I just leave the duplicate haplotypes in the file on separate lines and let it run that calculations that way? The analysis will run with the duplicates with no errors, but I wasn't sure if having them all in file versus specifically denoting replication would cause the output values to differ.
Thanks!
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