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Kalign is a fast and accurate multiple sequence package designed to align large numbers of protein sequences.

Kalign home page: KAlign

To use Kalign open a multiple sequence alignment file and select the Align with Kalign item in the context menu or in the Actions main menu. The following dialog appears:

     <img src="/wiki/download/attachments/7012361/Kalign Aligning.png"/>

The following parameters are available:

Gap opening 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.

Terminal 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.

Translate to amino when aligning - translates an alignment to amino when aligning.