What are some good programs for phylogenetic based on 1.8 million SNPs called across 48 taxa? Any suggestions for programs?

I have a SNP dataset called from 48 individuals across 4 species.  1.8 million SNPs.  I am looking for some opinions on the best programs to build a phylogeny of such a large dataset -- these SNPs...

06 June 2017 9,962 5 View