Hi @Sue,
I think you should be fine, as the MAFFT manual suggests that you can optionally use --p-parttree parameter above 10,000 sequences. However, --p-parttree parameter is required for anything above 1,000,000 sequences.
I think you should be generally fine just setting this, assuming you have at least a few thousand sequences. Not sure how well this would work with less than that though...
You can read more about the PartTree algorithm.
-Mike