I should construct a phylogenetic tree using a subset of SNPs hitting a certain gene. I tried
SNPhyl, but my vcf file is basically too small for this tool to run and I received the following error:
VCF file (../../../Data/nanog.vcf) is too small to run this script!
So, I was wondering if you have any recommendations for a tool that is able to generate a phylogenetic tree from a ~2MB vcf file.
With many thanks, Gökberk