Align with MUSCLE Element
MUSCLE is a public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.
Element type: muscle
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Mode | Selector of preset configurations, providing an option to optimize accuracy, speed, or a compromise between the two. The default favors accuracy. | MUSCLE default | mode | numeric |
| Available values are: 0 - for MUSCLE default 1 - for Large alignment 2 - for Refine only | ||||
| Stable order | Do not rearrange aligned sequences (-stable switch of MUSCLE). Otherwise, MUSCLE rearranges sequences so that similar sequences are adjacent in the output file, making the alignment easier to evaluate by eye. | True | stable | boolean |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input MSA
Name in Workflow File: in-msa
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| MSA | msa | msa |
And 1 output port:
Name in GUI: Multiple sequence alignment
Name in Workflow File: out-msa
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| MSA | msa | msa |