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.
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.
Connect the elements:
Result: The elements are connected with arrows.
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.
Result: After the schema has run, a blue notification has pop up.
Result: The file has been opened. It contains the result of the alignment with MUSCLE.