I am working with DnaSP with a large dataset (56kb of sequence scanned for
SNPs in 80 chromosomes). DnaSP limits each sequence input to ~32kb. So,
my data is not acceptable.
Not all my sites are polymorphic. I would like to input only the
polymorphic sites and then the length of the scanned sequence. Could
someone please suggest how I might do this using a Nexus or other file
format? I am also planning to use Arlequin and wonder if I can do the
same for that program.
I am no expert in population genetics but it seems I need the number of
bases scanned for certain population genetic parameters, so I am looking
for a way to include this in a smaller file. I have heard there may be
something called a "size block" in Nexus format but do not find it
mentioned in the original Maddison paper.
Any help you could offer would be greatly appreciated,
Department of Molecular Biotechnology
University of Washington