Hi,
I'm looking at genetic diversity from full mitochondrial genomes from 96 different sequences. While building the haplotype network in popart, it shows 6 sequences with identical mitogenomes. However, when I run analyses in Arlequin, it shows all unique haplotypes. Do these programs have different parameters for defining what is identical or not? I think the problem could be N's which popart might consider the same base as what is in the "identical sequence", but Arlequin will not. Thanks for any help.
Jacob