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MHCcluster 2.0 Server

The MHC genomic region in most species is extremely polymorphic. The distinct specificity of the majority of the MHC molecules remains uncharacterized. The MHCcluster is a tool to functionally cluster MHC class I molecules (MHCI) based on their predicted binding specificity. The tool provides highly intuitive heat-map and graphical tree-based visualizations of the functional relationship between MHC class I and class II variants.

For MHC class I, peptide binding predictions are made using NetMHCpan PMID 19002680.
For MHC class II, peptide binding predictions are made using NetMHCIIpan PMID 21073747.

View the version history of this server. All the previous versions are available on line, for comparison and reference.

Note, as of July 8, 2014 peptide binding predictions can be made using either NetMHCpan version 2.8, or NetMHCpan version 2.7 (the earlier default)


Number of peptides to include  

Number of Bootstrap calculations 

Fraction of peptides to include in correaltion analysis 

Select MHC class: 

Select NetMHCpan prediction method (only for class I)

Select allele set/loci/species to include in tree

Select Allele(s) or type allele names (ie HLA-A01:01) separated by commas (and no spaces)

or upload file with allele names (one name per line)

For list of allowed allele names click here List of MHC allele names.

or paste full length MHC protein sequence(s) in FASTA format into the field below:

or submit a file containing full length MHC protein sequence(s) in FASTA format directly from your local disk:


The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

  • MHCcluster, a method for functional clustering of MHC molecules. Martin Thomsen, Claus Lundegaard, Soren Buus, Michael Rasmussen, Ole Lund and Morten Nielsen
    Immunogenetics. 2013 Jun 18. [Epub ahead of print]


Scientific problems:        Technical problems: