How to Create Haplotype trees from Y-Chromosome SNP data

Question

[mattbawn]

I have 17 SNP calls from Y-Chromosome NGS data. How do I go about trying to construct a phylogenic tree? I have created a script that has tabulated the data regularly as a .csv file containing the coordinates and the reference and alternate nucleotide for each sample. I was trying to use the SNPhylo pipeline but the documentation is rather sparse.

Any ideas, suggestions would be gratefully received.

Thanks,
Matt