User GuidesSnapGene User Guide Pairwise and Multiple AlignmentRepeat an Alignment with an Alternate Algorithm, New Parameters or Changed Input

Repeat an Alignment with an Alternate Algorithm, New Parameters or Changed Input

How do I rerun an alignment with another alignment algorithm, changed parameters or changed sequence inputs?

This article describes steps to perform a realignment of a DNA multiple sequence alignment using an alternate algorithm. The same steps can be followed for protein multiple alignments, DNA pairwise alignments and protein pairwise alignments.

Create or Open an Alignment File

Create or open an alignment file. See this lesson to learn how to create an alignment - Create a Multiple Sequence Alignment.

Redo the Alignment

Click Alignments → Redo Alignments.

Choose whether to replace the existing alignment file or create a new alignment file. Click OK.

Change the alignment parameters or inputs.

You can:

  • Import new sequences and add them to the existing sequences.
  • Exclude (uncheck) previously used sequences, or
  • Change the algorithm for alignment.
  • Change advanced settings via the algorithm-specific Settings buttons.

Click "DNA Sequences" to uncheck or remove selected sequences.

Once configured, click Align to create the revised alignment.

View the New Alignment

View the new alignment, and if required, use the controls in the side panel to change the way the alignment is displayed.