feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

feat: optimize CASTp SASA with KDTree, add sequence input to CASTp + Structure Prep, ESMFold integration for unknown genes

feat: structure preparation pipeline — broken chains → SWISS-MODEL repair → PyMOL cleanup → fpocket + CASTp

feat: add CASTp pockets, SWISS-MODEL, ESMFold + fix Dockerfiles

feat: replace igv.js with custom SAM/VCF genome viewer

chore: remove samUrl prop from IgvBrowser (igv.js only supports BAM)

fix(ngs): dynamic locus + SAM-first igv.js for reliable genome browser

fix: igv.js white screen — CIGAR ops, qual strings, locus format

feat: add igv.js genome browser + proper 6-step NGS pipeline

feat: add full 6-step NGS pipeline + fix sequencing WinError 193

feat(landing): 'Stop tab-switching' hero + docking sample, drop stale New badges

feat(results): in-app share dialog + self-normalized dotplot scoring

feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron

feat(design): bioluminescent green+violet palette and re-tuned landing hero

feat(theme): dual light/dark mode with Apple light theme, toggle, and theme-aware viewers

feat(seq-tools): share colored MSA viewer across BLAST job, alignment tool, report, shared and phylo surfaces

fix(seq-tools): stop auto-scrolling on job completion, fix structure highlight & AlphaFold viewer loading

feat(seq-tools): wire motif scanner into BLAST, structure, alignment and dot-plot workflows

fix(seq-tools): only link motif highlights to structure when a protein UniProt accession is known

feat(seq-tools): motif categories & structure overlay, dot-plot scoring & features, cross-tool links

feat(seq-tools): add sequence utilities, motif scanner and dot plot tools with frontend pages

refactor(alignment): reuse shared parseAlignedFasta on alignment page instead of local copy

feat(alignment): show matched/mismatched/gaps/length stats across all alignment views via shared AlignmentStatsBar

feat(primers): add NCBI gene search + sequence retrieval, oligo QC and in-silico PCR verification with recharts graphs

feat(export): add downloads to ADMET, MD, pairwise, AlphaFold, docking, pathway, plus 4 new learn topics

feat(landing): add cursor glow to hero and hover/tap polish to analyze cards

fix(frontend): stop polling after job completion and surface AI rate-limit retry countdown

fix(function-predict): add BP term, real AA composition, JSON export, UniProt distinction, and /learn topic

fix(pathways): read enrichment results from projection response, add p-value and gene ratio

Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data

Refine design system: semantic color tokens, tiered motion, denser result cards, VinaLog toolbar

Add global/local BLAST modes, full-length pairwise alignment view, standalone pairwise tool

Add next/core-web-vitals ESLint config, fix unescaped entities

Polish tool pages: fix dead bg-glass-card classes, contrast on teal, confidence band tokens, RNA badge

Convert legacy light pages (auth, callback, shared, blast) and components to native dark tokens

feat(docking): show full AutoDock Vina log by default, no scroll cap

refactor(icons): migrate lucide-react to @phosphor-icons/react, remove dep

feat(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

feat(uniprot,domains): reviewed/organism filters + debounce/fast-path, PROSITE raw-sequence scan UI (3c,3d)

feat(alignment): multi-method MSA (clustalo/muscle/kalign/mafft/tcoffee) with method selector (3b)

feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu

fix(frontend): clear stale results, prefill-only bridges, and results-ready banners

fix(md): don't abandon long jobs after 5 min + trim workload

feat(frontend): roll design-system classes across all dashboard pages + fix sidebar toggle alignment

feat(md): clay simulation-parameter controls (force field, solvent, run length)

feat(md): temperature/KE, Rg and SASA traces; fix OpenMM in deployed image

feat(md): real OpenMM production runs with accurate Ca RMSD

feat: cross-feature auto-fill bridges — data flows between all tools via sessionStorage

feat: expanded Domain & Motif Analysis with all features and cross-project links

perf: parallelize post-BLAST steps + fast_mode Swiss-Prot toggle