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Aligns multiple sequence alignmen= ts (MSAs) supplied with Kalign. Kalign is a fast and accurate multiple sequ= ence alignment tool. The original version of the tool can be found onhttp:/= /msa.sbc.su.se.
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 wh= en closing a gap. | 54.90 |
Terminal gap penalty | The penalty to extend gaps from the N/C terminal= of protein or 5=E2=80=99/3=E2=80=99 terminal of nucleotide sequences. | 4.42 |
Bonus score | A bonus score that is added to each pair of alig= ned residues. | 0.02 |
Parameters in = Workflow 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= span>
The element has 1 input port:
Name in GUI: Input MSA
Name in Workflow&nbs= p;File: in-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |
And 1 <= /span>output port:
Name in GUI: Kalign result MSA
Name in Workflow&nbs= p;File: out-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |