MSA viewer
Open the online MSA viewer or upload an alignment file to get started.
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The viewer reads a multiple sequence alignment in your browser and displays its sequences as an interactive, color-coded residue grid. It also calculates the consensus sequence and conservation at each aligned position.
Click the upload area and select an alignment file, or drag and drop the file onto it. The viewer detects the alignment format and opens the sequences automatically.
You can open aligned FASTA, CLUSTAL, Stockholm, PHYLIP, and MSF files, including common extensions such as .fasta, .aln, .sto, .phy, and .msf.
Yes. The MSA viewer displays an existing alignment but does not align unaligned sequences. Create the alignment with a tool such as Clustal Omega, MAFFT, or MUSCLE before opening it here.
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Click the upload area above and choose an alignment file, or drag it onto the page. The viewer detects the format, lays the sequences out as a color-coded residue grid, and adds a consensus row and a conservation track. Hover over a column to read its position, conservation and consensus residue, and use the search box to filter sequences by ID.
Everything runs in your browser. The file is not uploaded, and no account is needed. The viewer shows an existing alignment and does not align sequences itself; for unaligned FASTA, run Clustal Omega, MAFFT or MUSCLE5 first and open the result here.
| Format | Extensions | Typical source |
|---|---|---|
| Aligned FASTA, A2M, A3M | .fasta, .fa, .fas, .faa, .fna, .afa, .mfa, .a2m, .a3m, .txt | MAFFT, MUSCLE, ColabFold and HHblits MSAs |
| Clustal | .aln, .clustal, .clw | Clustal Omega, ClustalW, EBI services |
| Stockholm | .sto, .stockholm | Pfam, Rfam, HMMER |
| PHYLIP | .phy, .phylip | Phylogenetics tools such as IQ-TREE and RAxML |
| MSF | .msf | GCG and older alignment software |
| SELEX, Vienna | .selex, .vie, .vienna | HMMER and RNA alignment tools |
Pick a scheme from the color menu above the alignment.
| Scheme | What the colors mean |
|---|---|
| ProteinIQ | Hydrophobic (blue), aromatic (darker blue), positive (green-teal), negative (pink), polar (sand), cysteine (purple) |
| Clustal | The familiar ClustalX coloring by residue class |
| Zappo | Physicochemical groups: aliphatic, aromatic, charged, polar, special conformations |
| Taylor | A distinct color for every amino acid |
| Hydrophobicity | A gradient from hydrophobic to hydrophilic |
| Charge | Positive K, R and H against negative D and E, with other residues neutral |
| Size | A gradient by side-chain volume |
| Nucleotide | A, C, G and T/U for DNA and RNA alignments |
| Monochrome | Letters only, no coloring |
The consensus row shows the most frequent residue in each column. A column where more than half the sequences have a gap shows a gap in the consensus.
The conservation track scores each column from 0 to 100% using Shannon entropy over the non-gap residues, scaled against the maximum entropy of 20 amino acids. A column where every sequence has the same residue scores 100%. Because the scale is set for proteins, a DNA or RNA column with all four bases in equal amounts still scores about 54%, so read nucleotide conservation relative to the rest of the alignment rather than as an absolute value.
| Conservation | What it usually means in a protein alignment |
|---|---|
| Above 90% | Invariant or nearly so; catalytic, structural or binding residues |
| 70 to 90% | Conserved with conservative substitutions |
| 50 to 70% | Variable but constrained |
| Below 50% | Freely variable; loops, disordered regions, surface positions |
Gappy columns lower the evidence behind a score, so a high score in a column that most sequences skip says less than the same score in a full column.
The display options menu groups the settings that change how the alignment is drawn.
| Group | Setting | Effect |
|---|---|---|
| Layout | Font size, ruler, residue numbers | Size of the grid and the position labels around it |
| Layout | Wrap rows, block width | Break the alignment into stacked blocks of a set width, as in a printed alignment |
| Order and focus | Sort by | Input order, name, or similarity to the consensus |
| Order and focus | Reference | Pin one sequence to the top and color only the residues that match it |
| Columns | Hide gappy columns, max gaps | Drop columns with more gaps than the threshold |
| Annotation tracks | Consensus, conservation | Show or hide the two tracks |
| Coloring | Match consensus as dots | Replace residues that match the consensus with a dot, so differences stand out |
| Coloring | Color above identity | Color a residue only when its column identity passes the threshold |
| Coloring | Dim variable columns | Fade columns below a conservation threshold |
Pinning a reference is the quickest way to read a mutant panel or an ortholog set against your sequence of interest. Dots for consensus matches work well for close homologs, where most columns are identical.
The export button saves the alignment as a PNG, JPG or SVG image with the current colors and settings. Choose the current view, the full alignment, or only the sequences that match your search. SVG keeps the letters as text, which is easiest to edit for a figure. The FASTA download writes the alignment back out as aligned FASTA.
An alignment is often the input to the next step. Build a tree with IQ-TREE, or check the structure behind a conserved region in the PDB viewer.