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 Genomics Workbench this is done by creating a comparison table:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Alignments and Trees (Image alignmentsandtrees)| Create Pairwise Comparison (Image pairwise_comparison)

This opens the dialog displayed in figure 20.16:

Image createpairwisecomparisonstep1v2
Figure 20.16: Creating a pairwise comparison table.

Select at least two alignments alignment to compare. A pairwise comparison can also be performed for a selected part of an alignment:

        right-click on an alignment selection | Pairwise Comparison (Image pairwise_comparison)

There are five kinds of comparison that can be made between the sequences in the alignment, as shown in figure 20.17.

Image createpairwisecomparisonstep2v2
Figure 20.17: Adjusting parameters for pairwise comparison.