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(pipeline): send alignment_mode from wizard to pipeline v2 API

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(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

Docking: flatten multi-chain obabel receptor output to a single model

Fix docking on Windows: resolve obabel from venv, use Windows Vina binary

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

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

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

docs(design): canonical design system doc + ui-ux-pro-max MASTER

chore(deps): add geist + @phosphor-icons/react

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

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

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(blast): honor program/db/max_hits params, accept DNA queries, poll cap 65 min

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

fix(md): raise production budget to 25 min so runs aren't clamped to ~3 ps

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(frontend): HUD glass design system + clay components

fix(md): reflect OXT across C-CA axis so GBSA stops NaNing on Linux CPU

fix(md): surface real OpenMM error message + traceback in fallback diagnostics

fix(md): add missing C-terminal OXT so unterminated termini (1TIM HIS 248) build in OpenMM

fix(md): BioPython fallback crash on Atom.element.name ('str' object has no attribute 'name')