MUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Mode | Selector of preset configurations, that give you the choice of optimizing accuracy, speed, or some compromise between the two. The default favors accuracy. | MUSCLE default |
| Stable order | Do not rearrange aligned sequences (-stable switch of MUSCLE). Otherwise, MUSCLE re-arranges sequences so that similar sequences are adjacent in the output file. This makes the alignment easier to evaluate by eye. | True |
Parameters in Workflow File
Type: muscle
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| mode | Mode | numeric Availables values are:
|
| stable | Stable order | 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 |