In SIFT dbSNP, separate scores are returned for orthologs and homologs. I thought an ortholog is a homolog, so I am a little confused. In the paper by Ng & Henikoff, they say:
"Although SIFT can choose sequences automatically, better prediction results may be obtained when all of the sequences that are provided are orthologous to the query protein. This is because inclusion of paralogous sequences confounds prediction at residues conserved only among the orthologues."
So, do homologs include both orthologs and paralogs?