As some of the samples are incredibly diverse they do not allow for a clear, concise and legible haplotype network.
Would it be appropriate to create a histogram of haplotype frequency.
While this would not show the phylogenetic perspective it would still provide a measure of how haplotypes are distributed.
Suggestions would be welcome.
Certainly you could use histograms but only a network will tell you how the haplotypes evolved. Could you do use both and refer branches to each histograms. Or use the pid chart method?
Thank you for your comment Patrice. While that would be possible the issue is to do with the number of SNPs between some of the clades. Some are in such high abundance that it makes for terrible interpreted viewing.
You can use pies from excel to presenting haplotypes and the percentage of each.
Ho Duo Xu, I have found a way to create a Hap pairwise distance matrix heat-map by connecting arlequin and R.
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