To align two sequences go to the Pairwise Alignment tab of the Options Panel:

Select two sequence from the original alignment, select the parameters and click on the Align button. The following parameters are available:

Sequences

The first and the second sequences for the Pairwise Alignment.

Algorithm

The algorithm of the Pairwise Alignment. There are two algorithms:

1. Hirschberg (KAlign) - algorithm has the following parameters:
   • Gap open penalty - indicates the penalty applied for opening a gap. The penalty must be negative.
   • Gap extension penalty - indicates the penalty applied for extending a gap.
   • Terminate gap penalty - the penalty to extend gaps from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
   • Bonus score - a bonus score that is added to each pair of aligned residues.
2. Smith-Waterman - the same algorithm, which is used for the Smith-Waterman Search (check the page for the algorithm details). The following parameters are available:
   • Algorithm version - version of the algorithm implementation. Non-classic versions produce the same results as classic but much faster. To use these optimizations our system must support these capabilities: OPENCL, SSE2 or SW_classic.
   • Scoring matrix - scoring matrix.
   • Gap open penalty - penalty for opening a gap.
   • Gap extension penalty — penalty for extending a gap.

Output settings

Settings of the output file:

• In the new window - create a new alignment and open it if checked or just align two sequences of the current  alignment if it is not.
• Output file - the result file path.