Hi all,
I'm trying to create a haplotype network for >300 sequences, >80 haplotypes and 8 groups.
I tried to use
R pegas
Fluxus Network
PopART
My data include informative indels and either I miss haplotypes (pegas and PopART) in the output or I can not assign groups automatically (Fluxus network).
Does anybody has experience with creating haplotype networks or give me hints for my issues for one of the programs?
Thanks in advance!
Thanks I tried to avoid the commercial version and doing it by hand is a mess since it's to many sequences
Apart from the editing/output problem, have you solved the InDels issue?
in PopART no,
in Pegas I got the right haplotype number now using
dist.dna(x,model="indel") now, but haplotNet is running for ages.
Any suggestions or are you running into similar problems?
I couldn't find a way to assign my populations automatically. Do you have a script to parse any dnaSP Output or one of the fluxus intermediate files?
I also face the similar issue about handling the informative indels. My data set carries VNTRs and I wanted to assign haplotypes based on VNTRs. PopArt by default masks the regions with gaps. Can anyone suggest some other tool or figure out some way in PopARt, that can address the question?
Hi Manoswini Dash ,
my solution was to use R with the package PEGAS: distance model “indelblock”, performing an iterative refinement for the smallest sum of distances.
described in https://www.pnas.org/content/115/34/8609#sec-10
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