I am looking for a way to build a haplotype network using SSR data. I have been using Poppr R package before, but I want to see the distance between isolates in nodes/steps. In Poppr the network uses gray scale method of showing how closely related isolates are, but using this approach it is hard to interpret how many steps are between individuals (I need this information). I can't find how to change it in poppr and looking for another solution. So far I have found few packages for sequence data using SNPs but not SSRs.
Will greatly appreciate any advice or ideas.
Thank you!
Olga
I suggest the EDENetworks. You can generate a network based on individual or population genetic distance.
In second plane, you can also do it by SplitsTree. With this software you can use a matrix of pairwise genetic distances.
Best,
I would like to second SplitsTree. We used it in the past with SNPs and SSRs after computing genetic distances with PHYLIP (Genedist package-http://evolution.genetics.washington.edu/phylip/progs.data.dist.html).
Hi Olga,
Have a look at PopART: http://popart.otago.ac.nz/index.shtml
Good luck!
Conny
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