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Select Tools –> Workflow Designer in the main menu.Result: The Workflow Designer window appears.
On the Elements tab of the Palette find the Read alignment element. It is located in the Data sources group and drag it to the Scene.Result: The element is shown on the Scene.

Workflow Designer Documentation v. 1.14.0 > How to Create and Run Workflow > dragged_elt.png

Repeat the previous step for the Write Alignment element from the Data sinks group and for the Align with MUSCLE element from the Multiple sequence alignment group.Result: All three elements are on the Scene.

Workflow Designer Documentation v. 1.14.0 > How to Create and Run Workflow > all_elts.png

Connect the elements:
- Drag an arrow from the output port of the Read alignment element to the Align with MUSCLE element.
- Drag an arrow from the output port of the Align with MUSCLE element to the Write alignment element.
Result: The elements are connected with arrows.

Workflow Designer Documentation v. 1.14.0 > How to Create and Run Workflow > arrows.png

Select the Read alignment element. In the Parameters area of the Property Editor click on the Value column of the Input files parameter:

Workflow Designer Documentation v. 1.14.0 > How to Create and Run Workflow > browse_input_files.png

And browse for an input file, e.g.Select the $UGENE\data\samples\CLUSTALW\COI.aln file.Result: The Input files value is set to the file’s path.
Select the Write alignment element and set the Output file, e.g. you can just enter result.aln.Result: All required schema parameters are set.

Click the Run schema button on the toolbar.

Workflow Designer Documentation v. 1.14.0 > How to Create and Run Workflow > run_schema.png

Result: After the schema has run, a blue notification has pop up.

Open the the result.aln file in UGENE.

Result: The file has been opened. It contains the result of the alignment with MUSCLE.