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I looking for software to conduct a haplotype network using cytochrome oxidase (CO1) mitochondrial sequence data to study population structure in Anopheles mosquitoes.

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The software you are looking for is Network 5.0.0.3

Phylogenetic Network Software . Network © Copyright Fluxus Technology Ltd 1999–2018. Retrieved from https://www.fluxus-engineering.com/sharenet.htm

Whilst its old code it is still regularly used in pop gen for example there guys here recently used it. It will do the job, although personally I think Google Fusion tables are very cool, but that is complicated to use properly. R has some cool stuff in this context BTW, but in context I'd keep it simple (i.e. Network 5)

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