Question: Phylogenetic tree construction from small sized SNP data
0
gravatar for gokberk
17 days ago by
gokberk60
gokberk60 wrote:

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

ADD COMMENTlink modified 17 days ago by Philipp Bayer6.3k • written 17 days ago by gokberk60
2
gravatar for Philipp Bayer
17 days ago by
Philipp Bayer6.3k
Australia/Perth/UWA
Philipp Bayer6.3k wrote:

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

ADD COMMENTlink written 17 days ago by Philipp Bayer6.3k

Yes, it worked, thanks a lot Philipp!

ADD REPLYlink written 17 days ago by gokberk60
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