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(seo): JSON-LD structured data — Organization/WebSite graph, SoftwareApplication+HowTo homepage, BreadcrumbList across tools

feat(branding): Synteny rebrand — new identity, signal-coded palette, and pipeline icons

fix(pipeline): stop abandoning slow NCBI BLAST jobs + EBI fallback

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(landing): trust & craft pass — sample result preview with confidence bands, honest service/status copy, unified CTA verbs, grouped database taxonomy, 44px nav touch targets, calmer motion (no chevron loop, glow under nav)

feat(ui): apple-design conformance — springs for micro-interactions, reduced-motion/transparency/contrast support, typography tracking

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

feat(dashboard): add parallax quick-tool cards and cursor glow effect

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

Fix AI model fallback chain and enrich share message with result details

Fix share links, persist wizard jobs, add AI interpretation fallback, animate landing

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

Restore DNA helix as full-window landing hero background, drop fake HUD readout

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

Refine dashboard shell: neutral sign-out hover, instrument footer status line

Redesign landing: asymmetric hero with instrument-window helix, bento features, route-style pipeline, restrained motion

Delete legacy !important Tailwind override layer from globals.css

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

Remove light/dark theme toggle (dark-only app), drop ThemeProvider + darkMode config, add accent-hover token

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

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