Buy License
Advanced pairwise comparison
For a given set of aligned sequences it is possible 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 the Workbench this is done by creating a comparison table.
Pairwise comparison parameters
There are four kinds of comparison that can be made between a sequences in the alignment.
- Gaps. Calculates the number of alignment positions where one sequence has a gap and the other does not.
- Differences. Calculates the number of alignment positions where one sequence is different from the other. This includes gap differences as in the Gaps comparison.
- Distance. Calculates the Jukes-Cantor distance between the two sequences. This number is given as the Jukes-Cantor correction of the proportion between identical and overlapping alignment positions between the two sequences.
- Similarity. Calculates the percentage of identical alignment positions to overlapping alignment positions between the two sequences.
The pairwise comparison table
The table shows the results of selected comparisons. Since comparisons are often symmetric, the table can show the results of two comparisons at the same time, one in the upper-right and one in the lower-left triangle.The following settings are available in the side panel:
- Contents
- Upper comparison. Selects the comparison to show in the upper triangle of the table
- Upper comparison gradient. Selects the color gradient to use for the upper triangle.
- Lower comparison Selects the comparison to show in the lower triangle. Choose the same comparison as in the upper triangle to show all the results of an asymmetric comparison.
- Lower comparison gradient. Selects the color gradient to use for the lower triangle.
- Diagonal from upper. Use this setting to show the diagonal results from the upper comparison.
- Diagonal from lower. Use this setting to show the diagonal results from the lower comparison.
- No Diagonal. Leaves the diagonal table entries blank.
- Layout
- Lock headers. Locks the sequence labels and table headers when scrolling the table.
- Sequence label. Changes the sequence labels.
- Text format
- Text size. Changes the size of the table and the text within.
- Font. Changes the font of the table.
- Bold. Toggles the use of boldface in the table.
