Phylogenetic tree construction from small sized SNP data

Question

[gokberk]

Hi all,

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

Answer 1

[Philipp Bayer]

TASSEL can make simple cladograms from SNP data, that could work? https://www.maizegenetics.net/tassel

[gokberk]

Yes, it worked, thanks a lot Philipp!