how to select reference when constructing a SNP-based phylogenetic tree

Question

[zhangdengwei]

Hi all,

I am new to phylogenetic tree. I have around 220 K. pneumoniae isolates. I adopted roary to extract their core genes, and now I wonder construct a phylogenetic tree based on SNP. Should I provide a reference for constructing the tree? If so, how should I select the reference genome? Any suggestion would be greatly appreciated!