Alignments can be created from sequences, sequence lists, existing alignments and from any combination of the three.
To create an alignment in CLC Main Workbench:
Toolbox | Alignments and Trees ()| Create Alignment ()
This opens the dialog shown in figure 13.1.
If you have selected some elements before choosing the Toolbox action, they are now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences, sequence lists or alignments from the selected elements. Click Next to adjust alignment algorithm parameters. Clicking Next opens the dialog shown in figure 13.2.