I was calculating SIFT Scores using SIFT Blink, but warnings were coming because of median scores suggesting to use SIFT Sequence tool. After using SIFT Sequence tool warnings for my mutations were not there because of the modified median scores calculated, but when I looked on MSA, the protein sequences used by SIFT were very diverse while my query was human protein.

I wanted to ask that whether scores calculated by using SIFT Sequence tool is acceptable by reviewers or not, when the MSA (Multi sequence alignment) has many diverse sequences?

Help will be appreciated

Thanks