Run multiple sequence alignment

Use this page when you want to import sequences into the MSA workspace, run AlignCove, review the alignment, and export the result or a tree view.

Before you start

  • Open the workspace where you want the MSA stored.
  • Switch to Alignments and open the MSA panel.
  • Make sure your input files are in a supported alignment format.

Import sequences into an MSA

  1. Click Import... in the MSA sidebar.
  2. In the import accessory, choose:
  3. Open As
  4. Import mode:
    • New MSA
    • Add Sequences to Current MSA
  5. Select one or more supported files.
  6. Confirm the import.

Import sequences for alignment

Import sequences for alignment

Import the sequence files you want to compare into a new or existing MSA workspace.

Check your result - The imported alignment appears in the MSA list. - The visible sequence count updates.

Run AlignCove

  1. In Preset, choose AlignCove.
  2. Click Run Alignment.
  3. Wait for the job to finish before you judge the output.

Check your result - The alignment canvas updates with the aligned sequences. - The alignment controls are active.

Review the alignment and export the file

  1. Use the alignment controls you need, such as zoom, color scheme, consensus score, or logo.
  2. Open the Export menu.
  3. Choose the output you want:
  4. FASTA...
  5. CLUSTAL...
  6. PNG Snapshot...

Review the alignment

Multiple sequence alignment viewer

Review the alignment viewer before you export anything so you can confirm the sequences align the way you expect.

Tip - Export only after the alignment view has fully rendered, especially for PNG snapshots.

Build and export a tree when needed

  1. Switch the MSA content view to Tree.
  2. Click Build Tree.
  3. Adjust the framing with Fit, Reset, or zoom controls as needed.
  4. Export the tree in the format you need:
  5. Export Newick
  6. Export SVG
  7. Export PNG

Check your result - The tree view renders and the export actions are available.

If it doesn't look right

  • Run Alignment is disabled:
  • Confirm an alignment with sequences is selected and no other run is already in progress.
  • Export options are disabled:
  • Select an alignment payload first.
  • Neighbor-Joining is unavailable or slow:
  • Reduce sequence count or choose a lighter method before retrying.