Proteasomal cleavage:

PAProC - Prediction Algorithm for Proteasomal Cleavages
Department of Immunology and Department of Biomathematics, Eberhard-Karls-University Tübingen - Tübingen, Germany
http://www.paproc.de/

NetChop - prediction of cleavage sites of the human proteasome
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetChop/

MAPPP - MHC-I Antigenic Peptide Processing Prediction (FragPredict)
Max Planck Institute for Infection Biology - Berlin, Germany
http://www.mpiib-berlin.mpg.de/MAPPP/

TAP binding:

TAPPred - prediction of TAP binding peptides
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/tappred/

MHC peptide binding:

RankPep - prediction of MHC binding peptides
Molecular Immunology Foundation
http://bio.dfci.harvard.edu/Tools/rankpep.html

MHCBench - benchmark MHC binding peptide prediction algorithms
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/mhcbench/

HLA Peptide Binding Predictions (BIMAS) - prediction of binding affinities for HLA class I molecules
BioInformatics & Molecular Analysis Section, CBEL, CIT and NIH - Bethesda, MD
http://www-bimas.cit.nih.gov/molbio/hla_bind/

PREDEP - MHC Class I epitope prediction
Department of Molecular Genetics and Biotechnology, The Hebrew University of Jerusalem - Jerusalem, Israel
http://margalit.huji.ac.il/Teppred/mhc-bind/index.html

nHLAPred - MHC Class-I binding peptide prediction
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/nhlapred/

ProPred-I - promiscuous MHC Class-I binding peptide prediction
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/propred1/

SVMHC - prediction of MHC class I binding peptides
Stockholm Bioinformatics Center, Stockholm University - Sweden
http://www-bs.informatik.uni-tuebingen.de/Services/SVMHC

EPIPREDICT - MHC class II binding peptide prediction
Institute of Immunology - Rikshospitalet, Oslo AND Dep. of Onkology/ Immunology, University Childrens Hospital - Tübingen, Germany
http://www.epipredict.de

ProPred - prediction of HLA-DR binding sites
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/propred/

NetMHC - prediction of binding affinities for HLA-A2 and H-2Kk
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetMHC/

NetMHCII - prediction of binding affinities for different HLA-DR
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetMHCII/

NetMHCpan - prediction of binding affinities for different HLA-A and -B
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetMHCpan/

SMM - prediction of high affinity HLA-A2-binding peptides
Boston University - Boston, MA
http://zlab.bu.edu/SMM/

POPI - prediction of immunogenicity of binding peptides of MHC class I and II
Institute of Bioinformatics, National Chiao Tung University - Hsin-Chu, Taiwan
http://iclab.life.nctu.edu.tw/POPI/

OptiTope - determination of an optimal set of epitopes with respect to overall immunogenicity in a specific individual or a target population
Division for Simulation of Biological Systems, University of Tübingen - Tübingen, Germany
http://www.epitoolkit.org/optitope

Mosaic Vaccine Tool Suite - design and assess vaccine candidate protein sequences
Los Alamos National Laboratory - Los Alamos, NM
http://www.hiv.lanl.gov/content/sequence/MOSAIC/

HLABinding - prediction of MHC class I binding peptides - NEW
Microsoft Research - Redmond WA
http://atom.research.microsoft.com/hlabinding/

Antigenic peptides:

Prediction of Antigenic Determinants - prediction of peptides likely to elicit an antibody response
Molecular Immunology Foundation
http://bio.dfci.harvard.edu/Tools/antigenic.pl
Additional information: http://bio.dfci.harvard.edu/Tools/antigenic.html

ANTIGENIC (EMBOSS package) - prediction of peptides likely to elicit an antibody response
Institut Pasteur - Paris, France
Search for "antigenic" at http://mobyle.pasteur.fr/cgi-bin/portal.py

BepiPred - prediction of linear B-cell epitopes
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/BepiPred/

DiscoTope - prediction of discontinuous B-cell epitopes
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/DiscoTope/

ElliPro - prediction of peptides likely to elicit an antibody response - NEW
National Institute of Allergy & Infectious Diseases - Bethesda, MD
http://tools.immuneepitope.org/tools/ElliPro/iedb_input

Antibody Epitope Prediction - prediction of continuous linear B cell epitopes- NEW
National Institute of Allergy & Infectious Diseases - Bethesda, MD
http://tools.immuneepitope.org/tools/bcell/iedb_input

CTL epitopes:

CTLPred - prediction of CTL epitopes
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/ctlpred/

NetCTL - prediction of CTL epitopes
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetCTL/

MHC-I processing predictions - prediction of a peptide's intrinsic potential of being a T cell epitope- NEW
National Institute of Allergy & Infectious Diseases - Bethesda, MD
http://tools.immuneepitope.org/analyze/html/mhc_processing.html

Epitope analysis :

Epitope Cluster Analysis - grouping of epitopes into clusters based on sequence identity - NEW
National Institute of Allergy & Infectious Diseases - Bethesda, MD
http://tools.immuneepitope.org/tools/cluster/iedb_input

Epitope Conservancy Analysis - determination of the fraction of protein sequences containing an epitope at a given identity level - NEW
National Institute of Allergy & Infectious Diseases - Bethesda, MD
http://tools.immuneepitope.org/tools/conservancy/iedb_input

Tumor antigens:

VaxiJen - prediction of tumor antigens - UPDATED
Edward Jenner Institute for Vaccine Research - United Kingdom
http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html