Folder Structure V3: Genome files are now normalized to use consistent, genome-identifier-based contig IDs and locus tags ({genome_id}_scf{n} and {genome_id}_{n:06d}). Use update_folder_structure from arx-tools to migrate. See Folder Structure for details.
Plotly-based Dotplot Viewer: The dotplot viewer has been rebuilt on Plotly. Gene annotations from GenBank files are rendered as arrows, scaffold tracks are color-coded, and keyboard shortcuts (arrow keys, +/-) and double-click-to-zoom are supported. See Dotplot.
Scoary-2 Gene Trait Matching: Gene trait matching now supports Scoary-2 as an additional method. Scoary-2 applies phylogenetic correction to account for population structure, reducing false positives in closely related datasets. Results open in an interactive per-trait viewer. See Gene Trait Matching.
Genome Similarity (ANI) page: A dedicated page for pairwise ANI calculations, with heatmap and dendrogram views and support for multiple backends (gendiscal, pyani-plus with fastANI/ANIb/ANIm/dnadiff). See Genome Similarity.
Async Gene Trait Matching and ANI: Gene trait matching and ANI calculations now run as background jobs, joining BLAST and phylogenetic trees. See Job Queues.
Job Queue Improvements: Jobs now show elapsed time, support pinning, display automatic titles, and are accessible via a bell icon in the navbar.
Tree Uploads: Trees can now be uploaded directly on the trees page in addition to being computed from genomes.
ANI Genome Uploads: Genome files (FASTA/GenBank) can be uploaded directly on the ANI page for pairwise similarity analysis without adding them to the library first.
Home Page Sunburst Filter and Search: The home page sunburst chart now supports filtering and searching by genome attributes.
Session Persistence: Selected genomes and BLAST inputs are remembered across page reloads using session storage.
NAV_LINKS: Custom navigation links can be added to the navbar via the NAV_LINKS environment variable. See Environment Configuration.
Dotplot DNA sequence display: DNA bases are now rendered directly on the alignment tracks when zoomed in sufficiently (≈8 px per base).
PostgreSQL benchmark command: A new python manage_arx.py postgres-benchmark command measures connection latency, write throughput, and read/aggregate speed to help diagnose database performance issues.
Changed
Dotplot: The underlying viewer has changed from the D3-based Dot to a Plotly-based implementation with more interactive controls.
Gene Trait Matching: Now runs as an asynchronous background job; results are stored and can be reopened from the Job Queues page.
Fixed
Annotation rendering in DNA viewer and gene detail pages.
Annotation import and search: Improved annotation import pipeline and search performance.