Hi all,
I am using POPART to create haplotype networks (TCS) for my data. I find that it automatically ignores gaps and hence advises that some haplotypes are the same sequence. Some of the sequences have insertions of adenine and I would like to consider these when creating the haplotype network. But I could not find a way for POPART to recognise these as separate sequences. Does anyone know if there is a way to consider such gaps/insertions in POPART? I have these considered in my input file, but cannot find an option for it when creating the network.
Dear Kristina,
to my knowledge PopArt never considers gaps. This is also a problem if not all of your sequences are full length, as PopArt will trim the ends automatically to the shortest. I suggest using Network (from Fluxus Technologies) instead as it treates indels as a separate mutation.
Best,
Martin
Dear Martin,
Many thanks for this. That what what I feared, which is a pity as I do generally prefer POPART. But I will look more into Network and use this instead then.
Kind regards,
Kristina
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