SNPs alignment as input

[mlarjim]

I have been using a core genome alignment as input of grapeTree stand-alone version, but it crashes when the alignment contains too many sequences because of a memory issue (I do not have enough memory resources in my computer).

So I was thinking about using a SNPs alignment (an alignment that just contains the nucleotides that have changed in any of the sequences), which is lighter than the cg alignment and less memory consuming. The resulting grapetree is slightly different Would that be a good approach for overcoming my memory issue?

Thank you in advance, Maria