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- 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.
- Smith-Waterman - the same algorithm, which is used for the Smith-Waterman Search (check the page for the algorithm details - the alignment process works in a same way as the searching process). 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_classicsupport SSE2.
- Scoring matrix - scoring matrix.
- Gap open penalty - penalty for opening a gap.
- Gap extension penalty — penalty for extending a gap.
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