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 onhttp://msa.sbc.su.se.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Gap extension penalty | The penalty for extending a gap. | 8.52 |
| Gap open penalty | The 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 penalty | The penalty to extend gaps from the N/C terminal of protein or 5’/3’ terminal of nucleotide sequences. | 4.42 |
| Bonus score | A bonus score that is added to each pair of aligned residues. | 0.02 |
Parameters in Schema File
Type: kalign
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| gap-ext-penalty | Gap extension penalty | numeric |
| gap-open-penalty | Gap open penalty | numeric |
| terminal-gap-penalty | Terminal gap penalty | numeric |
| bonus-score | Bonus score | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input MSA
Name in Schema File: in-msa
Slots:
| Slot In GUI | Slot in Schema File | Type |
|---|---|---|
| MSA | msa | msa |
And 1 output port:
Name in GUI: Kalign result MSA
Name in Schema File: out-msa
Slots:
| Slot In GUI | Slot in Schema File | Type |
|---|---|---|
| MSA | msa | msa |