MSA Viewer
Visualize and analyze multiple sequence alignments with residue coloring and conservation views.
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What is MSA Viewer?
MSA Viewer displays multiple sequence alignments in an interactive, color-coded format. Alignments from tools like Clustal Omega, MAFFT, or MUSCLE appear as rows of residues, with colors indicating amino acid properties or nucleotide identity. The viewer calculates conservation scores and consensus sequences, making it straightforward to identify conserved regions and sequence variation.
How to use MSA Viewer online
ProteinIQ's browser-based MSA Viewer renders alignments directly in the browser with no file size limits for registered users.
Input
| Input | Description |
|---|---|
Aligned Sequences | Pre-aligned sequences in FASTA or Clustal format. Paste directly or upload a file (.fasta, .fa, .aln, .clustal, .txt). |
The viewer accepts aligned sequences only. To align unaligned sequences first, use Clustal Omega, MAFFT, or MUSCLE5.
Viewer features
Color schemes
Residue colors highlight biochemical properties. Select a scheme from the dropdown:
| Scheme | Description |
|---|---|
ProteinIQ | Groups by hydrophobicity: hydrophobic (blue), aromatic (dark blue), positive (teal), negative (pink), polar (orange), cysteine (purple). |
Clustal | Classic ClustalX coloring familiar to longtime users. |
Zappo | Physicochemical property groupings. |
Taylor | Each amino acid gets a distinct color. |
Hydrophobicity | Gradient from blue (hydrophobic) to red (hydrophilic). |
Nucleotide | For DNA/RNA: A (blue), T/U (orange), G (green), C (red). |
None | No coloring, black text on white background. |
Hovering over a scheme in the dropdown previews its appearance before selection.
Conservation bar
The conservation bar above the alignment shows per-position conservation based on Shannon entropy. Taller bars indicate higher conservation (less variation), while shorter bars indicate variable positions. Hover over a bar to see the exact conservation percentage.
Consensus sequence
The consensus row below the alignment shows the most frequent residue at each position. Positions where gaps predominate show a gap character.
Navigation
| Control | Action |
|---|---|
Position input + Go | Jump to a specific column (1-indexed) |
| Arrow keys | Scroll horizontally through the alignment |
| Ctrl+Home / Ctrl+End | Jump to start or end of alignment |
| Font size slider | Adjust from 8px to 20px for readability |
| Search box | Filter sequences by ID |
Sequence selection
Click any sequence row to select it. Selected sequences can be exported independently. The Data tab provides a sortable table with residue counts and gap percentages for each sequence.
Export options
| Format | Description |
|---|---|
| FASTA | Standard aligned FASTA format (.fasta) |
| Clustal | Traditional Clustal alignment format (.aln) |
| PNG | Image of the alignment with current color scheme and display settings |
| CSV | Statistics table from the Data tab |
When sequences are selected, export downloads only the selected subset.
Interpreting conservation scores
Conservation scores range from 0% (completely variable) to 100% (identical across all sequences):
| Conservation | Interpretation |
|---|---|
| > 90% | Highly conserved, likely functionally important |
| 70–90% | Moderately conserved, may tolerate conservative substitutions |
| 50–70% | Variable, multiple amino acid types acceptable |
| < 50% | Highly variable, little selective pressure |
Completely conserved positions often indicate catalytic residues, structural requirements, or protein-protein interaction sites. Variable regions may represent loops, disordered regions, or sites of adaptive evolution.