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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.

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.
 

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• 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.
  
  

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

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