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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:
  • 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.

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

• 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.

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