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

fix: eliminate infinite re-render loop - remove ResizeObserver, fix ref prop conflict, simplify zoom/pan

fix: prevent infinite re-render loop in GenomeViewer (error #290)

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

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

refactor: require native samtools/minimap2, delete hand-rolled BAM/BAI code

fix: igv.js fetch BAM/BAI as Blobs, client-side SAM-to-BAM conversion, proper BGZF

fix: SAM-only igv.js track, indexed:false reference, debug logging

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

feat(ngs): pure-Python SAM to BAM converter with BGZF + BAI index for igv.js

fix: load igv.js from CDN instead of ESM import

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

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

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

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

feat(seq-tools): MSA match/mismatch/gap cell highlighting, consensus row and legend

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

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

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

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

fix(interactions): add evidence-type filter, JSON export, and learn tooltips to STRING-DB viewer

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

Add MSA pairwise refinement, new UI components (SmoothLoader, Reveal, CursorGlow, Parallax), rate-limit handling in AIInterpretation

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

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

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

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

style(theme): Geist fonts, AA-verified text tiers, 4-band confidence tokens

chore: frontend design polish (accent palette, remove glow/gradient utils), ignore installed skill trees, add opencode skills config

feat(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a)

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

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

feat(frontend): HUD glass design system + clay components