Kalign Aligning

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 option in the context menu or in the Actions main menu. The following dialog will appear:

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 sequences or the 5’/3’ terminal of nucleotide sequences.

  • Number of threads — the number of threads to use.

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