Release 5.0 of the Next-Generation IEDB Tools Website is now live! This release brings five new tools to the site (AXEL-F, Conservancy, PepSySco, Population Coverage, and RATE/COMBO-RATE), updates the T cell class I tool with NetMHCpan 4.2 and NetMHCphosPan, and adds many usability improvements.
Head over to https://nextgen-tools.iedb.org/ to try it out!
Release notes - 5.0 (Oct 2, 2026)
New Web Tools!
AXEL-F - Integrates MHC elution predictions with gene expression data to score peptides for likelihood of presentation. Start from either a list of peptides or FASTA protein sequences, with a configurable peptide length. Expression values can be provided directly or looked up by gene name.
Conservancy - Calculates how conserved a set of epitopes is within a given set of protein sequences, at a user-defined identity threshold. The alignment details table highlights mismatched residues so results can be scanned quickly.
PepSySco - Predicts how likely it is that a peptide can be synthesized successfully. Useful as a final check before ordering peptides. Results can be filtered by score.
Population Coverage - Calculates the fraction of a population expected to respond to a set of epitopes, based on their HLA restrictions. New in this version:
- Choose from multiple population frequency datasets: Allele Frequency Net Database (AFND), the LJI Cohort, and NMDP - or upload your own population frequency table.
RATE / COMBO-RATE - Identifies the most likely HLA restriction for T cell epitopes, using response data and HLA typing from multiple donors. COMBO-RATE extends this to allele combinations and can optionally add HLA binding predictions to the results.
Updated Web Tools!
T cell, class I - Now includes NetMHCpan 4.2 (EL and BA) and NetMHCphosPan, for predicting binding of phosphorylated peptides. Phosphorylated residues are marked with lowercase s, t, or y (e.g., EESDPPtYK).
New Pipelines!
With the new tools, the following pipelines are now enabled:
- T Cell Class I, T Cell Class II → Population Coverage (peptides and their alleles are collapsed automatically into the input format Population Coverage expects)
- T Cell Class I, T Cell Class II, Cluster, PepMatch, PepX, PHBR, Mutated Peptide Generator → AXEL-F
- Conservancy → T Cell Class I, T Cell Class II, Cluster, PepMatch, PepX, AXEL-F, PepSySco
- AXEL-F → Cluster, PepMatch, PepX, Conservancy, PepSySco
- Most peptide-producing tools → PepSySco
New Features!
- Input Preview - Before running a downstream pipeline step, a new “Input Preview” button shows exactly what data will be passed in from the previous step.
- Updated homepage and tools menu - Taglines for every tool on the All Tools list, a reordered tools menu, and “new” badges on this release’s tools.
- Documentation - User documentation for all of the new tools, a tutorial section for new users, dated release notes, a link to the latest release from the docs, and citation links for every tool.
- Support - Help links now go to the IEDB support forum (https://discuss.iedb.org) instead of email.
- PepMatch - Upgraded to PepMatch v1.17.2, which results in a substantial speedup.
New/Updated Standalones!
As companions to the new web tools, command-line versions of AXEL-F, Conservancy, PepSySco, Population Coverage, and RATE/COMBO-RATE are available from our Downloads page. The T cell, class I standalone has been updated with NetMHCpan 4.2 and NetMHCphosPan. All standalones now use a consistent output style on the command line, and the Downloads page lists the new packages.