Release Notes ============= Tracking changes and improvements across software versions. v3.2.0 (2026-03-26) ------------------- - Added VOG marker search module (``markers.py``): user proteins against VOGDB via MMseqs2 profile search - Added VOG-based host domain override: per-realm votes of user sequences can override the DB default domain when ≥80% of VOG hits vote for a different domain - Added VOG realm and taxonomy support throughout resolver and GBGA: VOG hits now contribute to realm identification and rank-level taxonomy assignments - Filled in mixed-realm Archaea distance thresholds that were previously disabled v3.1.8 (2025-12-20) ------------------- - vConTACT3 paper published at Nature Biotechnology! Update relevant locations - Updated exports to use lazy importing, hopefully reducing the resource requirements just *loading* vcontact3 v3.1.7 (2025-10-24) ------------------- - Update database versions allowed v3.1.6 (2025-10-22) ------------------- - Added extensive docstrings for all (?) functions and classes. Type hints have not yet been updated - Added bypass to allow vcontact3 installation when ete3 package is incorrectly installed v3.1.5 (2025-09-25) ------------------- - Rewrite upper and lower taxonomy assignments due to bug in propagating labels hierarchically. It is strongly recommended to update to this version. - Changed how novel prediction placeholders are structured. Upper ranks (e.g. kingdom, phylum, class) now use "unplaced__of_" and only lower ranks (e.g. order, family, subfamily, genus) start numbering. v3.1.4 (2025-08-17) ------------------- - Fix versioning for Bioconda install, which prevented version from being identified from git tag (pip was still fine) - Expose option to allow users to set maximum iterations to resolve multi-realm components v3.1.3 (2025-06-25) ------------------- - Update build and versioning system for package - Add Singelvaria - Update docs with recent changes v3.1.2 (2025-06-18) ------------------- - Add funding acknowledgements to docs - Add & expose centroid export option v3.1.1 (2025-06-13) ------------------- - Fix downloading from list v3.1.0 (2025-06-13) ------------------- - Add ANI export option - Add vclust as "optional" dependency - Switch from using setup.py to pyproject.toml - Update DB versions in docs - Restructured how package is run through the main function - Implement new build and versioning system. Instead of manually encoding version in several locations (= source of failure), git version tag is 'single source of truth' - Update recent changes to options and other changes in docs v3.0.5 (2025-06-05) ------------------- - Implemented new DB versioning system which identifies installed package version and evaluates it against DBs and their compatibility range - Added docs site to README - Change realm logic and which realms are handled by GBGA - Begin adding mixed-realm distance thresholds, allowing for user (and environmental) situations where multiple realms cannot be reliably disentangled - Fixed edge value reporting during identification of mixed-realm components, which prevented breaking at the appropriate limit - Fix category issue where new categories being added weren't being identified - Change fastcluster version to improve compatibility v3.0.3 (2025-05-29) ------------------- - Remove unnecessary imports and legacy code v3.0.2 (2025-05-29) ------------------- - Add back in NetworKit for processing extremely dense and large graphs for calculating connected components (in order to establish mutli-realm components) v3.0.1 (2025-05-29) ------------------- - Burn and rebuild resolver + GBGA modules. Use sparse matrices over 3rd party networks. Update iteration logic to resolve components. H5 for files. Integrate all network layers into single view. Fix gene + component realm identification. - [extensive other modifications] v3.0.0b74 (2024-12-30) ---------------------- - Apply default realm to final predictions. Was used and calculated, but ignored while writing the final file v3.0.0b (2024-11-02) ---------------------- - Addition of *Monodnaviria* for eukaryotes v3.0.0b (2024-10-31) ---------------------- - Addition of *Monodnaviria* for prokaryotes Future Work =========== These are planned updates and/or features. **There is no guarantee that these will be implemented, nor should be considered expectation of**, but *are* actively being worked on. * Enable newick export handling * More "useful" interactive network/graph with D3js * Improved memory handling * Filtering exports on user-defined labels (e.g. "Rudiviridae" would filter profiles, graphs, networks, etc) * **No-database / reference-free mode** — allow vConTACT3 to run without a reference database, performing de novo clustering and network construction on user genomes only (no taxonomy assignment). Useful for exploratory analyses or datasets from under-represented taxa. * **Unified database support** — the unified (cross-domain) database is partially implemented; remaining work is automatic host-domain detection so that the correct realm-level thresholds are selected without requiring the user to specify ``--db-domain`` explicitly. * **User-supplied custom reference databases** — allow users to provide their own curated set of reference genomes (formatted as a vConTACT3-compatible database) to supplement or replace the built-in RefSeq releases. This enables targeted analyses against taxon-specific reference sets. Development priorities are based on community feedback and internal benchmarking. Contributions or feature requests are welcome via the `issue tracker `_.