I've used SNPrelate but only for identity by descent analysis, thus it worked with .vcf file formats. And as I understand the package is mainly for that type of analysis and to do genomic PCAs.
what type of data are you using? NGS?
If you want to build a phylogeny with SNP data I would first recommend RAxML instead, also you should produce your sub-dataset of "non-synonymous SNPs" and then work the softwares on that sub-dataset.
Also just a remainder that for the phylogeny you should use the whole sequences and not exclusively the SNPs (sorry if this is obvious but I did this mistake in the past, so I'm just letting it here :) )