Hi all,
I'm analyzing the same dataset in PopArt, to create haplotype networks, and Arlequin for some statistics. My sequences contain missin data and indels and I left them there. When I look to the shared haplotype, results are different between the two softwares: most of thw shared haplotypes are the same, but not always.
What could be the problem?
Thank you!
The only way to really tell what is going on is to look at the specific cases in which e.g., sequences A and B are called as unique in one program and not the other.
Since you specifically mention the presence of missing/ gap characters, it would be worth looking into the manuals for the two programs and discovering how they handle those cases. Are the characters themselves simply masked? Whole columns removed? State space of haplotypes expanded? Also linked a paper by Joly et al. (2007) that may be of interest
Article Haplotype Networks Can Be Misleading in the Presence of Missing Data
Perhaps this might help:
https://www.youtube.com/watch?v=7yQ5N9fpTSA&t=36s
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