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.
Number of iterations — specifies the number of iterations.