I cannot get SNPYHLO to work - keeps throwing errors (maybe because I work with a non-model organism) and the documentation is very limited. snpTree requires read files and/or assembled genomes instead of vcf files. SNPRelate works (yeah!); however, I would like to confirm the results with another tool and also try to make a prettier plot. Any suggestions?
I found a couple of old posts like this one but I wondered if there really aren't any new tools out that simplify the task.