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<li><div tabindex="0" role="link" aria-label="Current page">NCBI MSA Viewer 1.25.3</div><div></div></li>
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<h1>NCBI Multiple Sequence Alignment Viewer</h1>
<p>The NCBI Multiple Sequence Alignment Viewer (MSA) is a graphical
display for nucleotide and protein sequence alignments.</p>
<h3>Review <a href="/tools/msaviewer" target="_blank">documentation</a> or watch <a href="https://www.youtube.com/watch?v=ILAoBRE9eSA" target="_blank">a video tutorial</a>.</h3>
<p>To see your own alignment, <input type="button" id="mainshow-btn" background-image = "images/upload.png" background-repeat = no-repeat background-position = left padding-left=16px
value="Upload" onclick="location.href='?appname=ncbi_msav&openuploaddialog'"/> your data</p>
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<h3>Examples of various alignment styles:</h3>
<ul style="line-height:1.4">
<li><a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/protein.gbp">Protein alignment with no anchor set</a></li>
<li>
<a href="?anchor=ACI28628&url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/protein.gbp">Protein alignment, anchor set to ACI28628</a>
</li>
<li>
<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/kinases_100_seq_updated.aln">Protein alignment using FASTA format from the MUSCLE program</a>
</li>
<li>
<a href="?rid=MJFN70DX013">Nucleotide alignment from Blast RID with query set as anchor; primate genomic, mRNA, and BAC sequences</a>
</li>
<li>
<a href="?rid=MJRDFGTD013">Protein alignment from Blast RID, metazoan proteins belonging to the LIN37 protein family</a>
</li>
<li>
<a href="?id=AY028675.1">Alignment of prion protein gene sequences from S. cerevisiae PopSet</a>
</li>
<li>
<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/d3.gbp&anchor=ABW74619">Polyprotein alignment with anchor, Dengue virus 2</a>
</li>
<li>
<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/dengue_nucleotide.asn&consensus=true">Genomic alignment with consensus, Dengue virus 1</a>
</li>
<li>
<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/non_canonical_Flu_nonambig.asn&coloring=nss&datasource=local">Alignment of nucleocapsid coding region, Influenza A virus (nonsynonymous substitutions coloring)</a>
</li>
<li>
<a href="?url=https://www.ncbi.nlm.nih.gov/projects/msaviewer/data/flu_H1N3_Canada_non_ambig_consensus.fa&coloring=nss">Alignment of polymerase PB1 coding region, Influenza A virus (nonsynonymous substitutions coloring)</a>
</li>
</ul>
<h3>You can also embed Multiple Sequence Alignment Viewer on your own page. Following are demo pages with embedded MSA Viewer</h3>
<ul style="line-height:1.4">
<li><a href="demo/demo_static.html">Static embedding</a></li>
<li><a href="demo/demo_dynamic.html">Dynamic embedding</a></li>
<li><a href="demo/demo_sv.html">Interaction with SV on the same page</a></li>
<li><a href="demo/demo_events.html">MSAV event handling</a></li>
<li><a href="demo/demo_coloring.html">Different coloring options</a></li>
<li><a href="demo/demo_mapping.html">Alignment Coordinate transformation</a></li>
<li><a href="demo/demo_consensus.html">Consensus parameters</a></li>
<li><a href="demo/demo_sort.html">Sorting parameters</a></li>
<li><a href="demo/demo_columns.html">Columns re-arranging</a></li>
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