Pairwise comparison

For a given set of aligned sequences it is possible to make a pairwise comparison in which each pair of sequences are compared to each other. This provides an overview of the diversity among the sequences in the alignment.

In CLC Main Workbench this is done by creating a comparison table:

        Toolbox | Alignments and Trees (Image alignmentsandtrees)| Create Pairwise Comparison (Image pairwise_comparison)

This opens the dialog displayed in figure 13.16:

Image createpairwisecomparisonstep1v2
Figure 13.16: Creating a pairwise comparison table.

If an alignment was selected before choosing the Toolbox action, this alignment is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove elements from the Navigation Area. Click Next to adjust parameters.