Hello People,

I am new to RAD-seq analysis and I've 100 samples of RAD-seq paired end double digest data from single population. I ran ipyrad and have got different output formats (vcf, loci, geno, phy, str etc.). Now I'm not able to generate graphs. I want to do qtl mapping, parsimony analysis, phylogenetic analysis, population structure and all possible downstream analysis.

Please suggest me tools and methods to generate graphs from my ipyrad outputs.

Thanks !!