This workflow performs multiple sequence alignment with MUSCLE algorithm and saves the resulting alignment to Stockholm document. Source data can be of any format containing sequences or alignments. To use this workflow, you need to specify locations for input and output file(s). To do this, select a corresponding task, so its' parameters appear in Property Inspector panel, and specify desired value(s) for "URL" parameter. Then you can launch the workflow with pressing Ctrl+R keys.
Also, if required, you can change parameters. Use the workflow wizard to guide you through the parameters setup process. The first wizard page will appear when you click on the Show wizard button on the Workflow Designer toolbar: