MSA Viewer parses and visualizes FASTA / Clustal / Stockholm 1.0 alignments entirely client-side. The main residue grid uses Canvas (100% base) for 60fps scrolling at 1,000+ columns × 100+ sequences; ruler, tooltip, and domain overlays sit on an SVG decoration layer. Fractional Gap-Penalized Shannon entropy (default) plus JSD (Capra-Singh 2007 BLOSUM62 background) and % identity, ClustalX (Thompson 1997 11-group conservation thresholds, pre-computed column profiles for O(1) lookup), Zappo, Taylor, Kyte-Doolittle hydrophobicity, and a conservation gradient — zero external chart / MSA libraries.

(1) Alternative to Jalview (Java desktop install), BioJS MSAViewer (English-only embed), and UGENE (heavy GUI) — instant in-browser + Korean primary (2) Inspect Pfam / InterPro alignments without uploading sequences to external servers (3) Validated against Globin / PKC kinase / 7TM GPCR canonical datasets (4) Reuses Phase 1 `_common/sequence.ts` + `_common/svg.ts` helpers → entry point for future MSA algorithms (BLOSUM matrices, AAindex, etc.)

① Upload FASTA / Clustal / Stockholm (or click "Load Globin demo") ② Pick color scheme (default: ClustalX, Thompson 1997 11-group thresholds) ③ Choose conservation algorithm: • Shannon (Gap-penalized) — default (AL2CO standard) • JSD (BLOSUM62) — functional residues (Capra-Singh 2007) • % Identity — simple modal frequency ④ Gap mode: Penalize (default) / Ignore / Include (21st residue) ⑤ Consensus threshold: 50 / 70 / 90% with guide symbols (`+` `.` `-`) ⑥ Zoom (8 / 12 / 16 px) + toggle residue text ⑦ Domain annotation: `>SeqA: 10-45, Kinase, #ff0000` (one per line) ⑧ Export: FASTA / Clustal round-trip + PNG (Canvas DPI-corrected) + JSON

Example 1) Globin family (human HBB / HBA / MYG) → Load demo → His F8 proximal histidine column S_norm ≥ 0.95 → ClustalX coloring applies immediately Example 2) PKC kinase family (5 sequences × ~300 columns) → DFG motif column conservation ≥ 0.9 → ClustalX yellow / red blocks → Glycine-rich loop visually confirmed Example 3) 7TM GPCR Rhodopsin family (20 seq × ~400 col) → TM1-TM7 conserved blocks automatically visualized → Conservation gradient highlights loop regions Example 4) Pfam PF00571 CBS domain (Stockholm) → `#=GC SS_cons` rendered automatically (α-helix `H` / β-strand `E`) → Active site highlighted via domain annotation