Create an alignment

Alignments can be created from nucleotide or protein sequences, sequence lists, existing alignments and from any combination of the three.

To create an alignment in CLC Genomics Workbench:

        Select Sequences to Align | Toolbox in the Menu Bar | Classical Sequence Analysis () | Alignments and Trees ()| Create Alignment ()

   or  Select Sequences to Align | Right-click any selected sequence | Toolbox | Classical Sequence Analysis () | Alignments and Trees ()| Create Alignment ()

This opens the dialog shown in figure 3.2.

Figure 3.2: Creating an alignment.

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 3.3.

Figure 3.3: Adjusting alignment algorithm parameters.