The Compare Proteins tool compares some major attributes like Subcellular location, Gene Ontology, Pfam Domian, Amino-acid composition, Molecular weight etc. within the proteins
The Compare Epitopes tool compares properties like Epitope, Combined Score, MHC I ALLELES, MHC II ALLELES,Conservancy, Allergicity, Antigencity, Toxicity, Hydropathicity, Hydrophilicity