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CHAPTER 3. ALIGNMENT OF SEQUENCES
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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.
3.1.1
Gap costs
The alignment algorithm has three parameters concerning gap costs: Gap open cost, Gap
extension cost and End gap cost. The precision of these parameters is one decimal place.
• Gap open cost The penalty for introducing gaps in an alignment.
• Gap extension cost The penalty for every extension past the initial gap.