nexus file for SNP data

Question

[scho249]

Hi Biostars people,

I want to use splitstree 4 to do some hybridization analysis and build tree using my SNP data. As an input file, it requires nexus file format. I did some searching and managed to convert my vcf file to 'standard' nexus file format. But I am confused in it's concept...

I believe that standard nexus file was for trait data not SNP... And if it store SNP data, it stores the state of the genotype:

aa: 0 ab: 1 bb: 2

This was how I converted my SNP vcf file to nexus file... But I thought genotype aa should be accounted more related to ab than bb, not having same distance...

could you tell me is there another way to store snp data to nexus file or what I am doing is correct?

Shane