> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.

# Sequence Alignment

> Align multiple sequences to identify conserved regions

Align sequences and search sequence databases to reveal evolutionary and functional
relationships. These tools build multiple sequence alignments that expose conserved regions
and motifs, and search large databases for homologs. The resulting alignments are also a
standard input for alignment-based structure prediction.

* **Input:** a set of related sequences, or a query sequence plus a database to search.
* **Output:** a multiple sequence alignment, or ranked homology hits with similarity statistics.

<div class="tool-catalog-grid">
  <a href="/docs/tools/sequence-alignment/blast" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/blast/carousel.png" alt="" loading="lazy" />

    <div class="tool-card-org-row"><span class="tool-card-org tool-card-org-light" style={{background: "#c0c0c0"}} title="NCBI"><img src="https://mintcdn.com/bio-pro/_UGa2jUMKeVPCbLk/assets/images/cached/6c0bd51170aa.png?fit=max&auto=format&n=_UGa2jUMKeVPCbLk&q=85&s=aece837308f5961d47623da652f395a2" alt="" class="tool-card-org-logo" width="200" height="200" data-path="assets/images/cached/6c0bd51170aa.png" /> NCBI</span></div>
  </a>

  <a href="/docs/tools/sequence-alignment/mafft" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/mafft/carousel.png" alt="" loading="lazy" />

    <div class="tool-card-org-row"><span class="tool-card-org" style={{background: "#DC2626"}} title="RIMD"><img src="https://mintcdn.com/bio-pro/_UGa2jUMKeVPCbLk/assets/images/cached/794c83bf4b6c.jpg?fit=max&auto=format&n=_UGa2jUMKeVPCbLk&q=85&s=4a04d6eae9054dea287479ded27a661b" alt="" class="tool-card-org-logo" width="400" height="400" data-path="assets/images/cached/794c83bf4b6c.jpg" /> RIMD</span></div>
  </a>

  <a href="/docs/tools/sequence-alignment/mmseqs2" class="tool-catalog-card">
    <img noZoom class="card-art" src="https://proto-bio.github.io/proto-assets/images/tool/mmseqs2/carousel.png" alt="" loading="lazy" />

    <div class="tool-card-org-row"><span class="tool-card-org" style={{background: "#2E86C1"}} title="Steinegger Lab"><img src="https://mintcdn.com/bio-pro/UeudeF7pW-Dj-pIN/assets/images/cached/5e3c631c9751.png?fit=max&auto=format&n=UeudeF7pW-Dj-pIN&q=85&s=5b9aab8b7ad1af8d3310a125bc9e540c" alt="" class="tool-card-org-logo" width="200" height="200" data-path="assets/images/cached/5e3c631c9751.png" /> Steinegger Lab</span> <span class="tool-card-org" style={{background: "#116656"}} title="Söding Lab"><img src="https://mintcdn.com/bio-pro/_UGa2jUMKeVPCbLk/assets/images/cached/ff28b89e17f3.png?fit=max&auto=format&n=_UGa2jUMKeVPCbLk&q=85&s=4c430d789fb73ff3fee2ef1fb75dc90b" alt="" class="tool-card-org-logo" width="200" height="200" data-path="assets/images/cached/ff28b89e17f3.png" /> Söding Lab</span></div>
  </a>
</div>