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:
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.