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Aligns multiple sequence alignments (MSAs) supplied with Kalign. Kalign is a fast and accurate multiple sequence alignment tool. The original version of the tool can be found on

Parameters in GUI

ParameterDescriptionDefault value
Gap extension penaltyThe penalty for extending a gap.8.52
Gap open penaltyThe penalty for opening/closing a gap. Half the value will be subtracted from the alignment score when opening, and half when closing a gap.54.90
Terminal gap penaltyThe penalty to extend gaps from the N/C terminal of protein or 5’/3’ terminal of nucleotide sequences.4.42
Bonus scoreA bonus score that is added to each pair of aligned residues.0.02

Parameters in Workflow File

Type: kalign

ParameterParameter in the GUIType
gap-ext-penaltyGap extension penaltynumeric
gap-open-penaltyGap open penaltynumeric
terminal-gap-penaltyTerminal gap penaltynumeric
bonus-scoreBonus scorenumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: Input MSA

Name in Workflow File: in-msa


Slot In GUISlot in Workflow FileType

And 1 output port:

Name in GUI: Kalign result MSA

Name in Workflow File: out-msa


Slot In GUISlot in Workflow FileType



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