Aligning with MUSCLE
Task Name: align
Performs multiple sequence alignment with the MUSCLE algorithm and saves the resulting alignment to a file. Source data can be of any format containing sequences or alignments.
Parameters:
| Parameter | Description | Default Value | Type |
|---|---|---|---|
| in | Input alignment [Url datasets] | ||
| max-iterations | Maximum number of iterations (using ‘2’ by default) | 2 | Number |
| mode | Selector of preset configurations, that give you the choice of optimizing accuracy, speed, or some compromise between the two. The default favors accuracy (using ‘MUSCLE default’ by default) | MUSCLE default | String |
| range | Whole alignment or column range, e.g., 1..100 (using ‘Whole alignment’ by default) | Whole alignment | String |
| stable | Do not rearrange aligned sequences (using ‘True’ by default) | True | Boolean |
| format | Document format of output alignment (using ‘clustal’ by default) | clustal | String |
| out | Output alignment [String] |
Example:
ugene align --in=test.aln --out=test_out.aln --format=clustal