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Old 01-09-2018, 12:24 PM   #1
Location: Germany

Join Date: Mar 2013
Posts: 35
Default Haplotype network indels HELP!

Hi all,
I'd like to create a haplotype network including 8 different groups. I have 326 sequences and 84 haplotypes. Some of the haplotypes only differ in indels, but they are real!
I tried R pegas and failed, because some of the haplotypes colapsed (maybe because of indels?)
I tried fluxus Network but couldn't find a way to automatically assign groups (sequence IDs contain group tags).
I used Popart, but again not all haplotypes are resolved correctly and here I can see, that indels are treated as "undefined states". Grouping was no problem since it's easy to parse a nexus file (*.mfa -> *.nex DNAsp) and include "traits".
Could someone please give me advice?!

Thanks in advance
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