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 alternative 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.
In the dialog that opens, choose whether to replace the existing alignment file or create a new alignment file, then 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.
- Select sequences and use the "Move:" controls to set a different order.
- Change or add algorithms for alignment.
- Change advanced settings via the algorithm-specific Settings buttons.
Once configured, click Align to create a 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.
