KEDROS
A comparative genomics workspace built by CGLab (IMBB-FORTH, Heraklion) and CGMLab (CBGP, Madrid).
About the tool
KEDROS is a comparative genomics platform for asking which protein families each organism carries, and what that pattern says about function and evolution. It runs against a local UniProt Reference Proteomes database enriched with Pfam-A HMM search results computed in-house. Once the database is set up, queries run entirely offline — no internet needed.
Source code & documentation: github.com/cgenomicslab/kedros.
It provides these analysis modules, plus sequence/domain utilities:
| Module | What you get |
|---|---|
| Phylogenetic Tree | Fetch sequences by Pfam/taxon, upload your own FASTA, or both merged together → align (MAFFT) → tree (FastTree/IQ-TREE) → interactive D3 viewer or ETE4 explorer with domain shapes. |
| Functional divergence | Scored automatically on every tree, from the alignment it was built from: which positions are conserved family-wide (JSD), which are fixed within each subfamily but differ between them (GroupSim), and which tell you the subfamily outright (MI). Top sites can be drawn as a column track beside the tree. |
| Clade actions | Pick a branch and extract its sequences, re-align and rebuild it as its own tree, or test what sets it apart from the rest of the tree — by Pfam domain, or by KEGG pathway and COG category via eggNOG-mapper. |
| Presence / Absence | Taxa × Pfam profile heatmap; drill into any cell for sub-profiles or domain architecture breakdown. |
| High-Res Profile | Partition gene trees into subclade (paralog) groups — by depth, manual MRCA, node path, or automatic duplication detection — and profile each subclade separately across taxa. |
| Discovery | Which protein families are present across one group of organisms and absent from another — drug targets, insecticide targets, metagenomic markers, or anything that tracks a phenotype. Ranked with Fisher exact p/q values, with an optional GO condition. |
| Utilities | Standard retrieval, HMM search, accession lookup, domain coordinates, GO→domain profiles, and branch extraction. |
Contributors
KEDROS is developed by the Comparative Genomics Lab (CGLab) and the Comparative Genomics and Metagenomics Lab (CGMLab).