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• Select Tools –> Workflow Designer or File->New worflow items 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.

<center>
  <img src="/wiki/download/attachments/1474815/dragged_elt.png"/>
</center>

• 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. 

<center>
  <img src="/wiki/download/attachments/1474815/all_elts.png"/>
</center>

• 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.

<center>
  <img src="/wiki/download/attachments/1474815/arrows.png"/>
</center>

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

<center>
  <img src="/wiki/download/attachments/1474815/browse_input_files.png"/>
</center>

• 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 workflow parameters are set.

• Click the Run workflow button on the toolbar.

<center>
  <img src="/wiki/download/attachments/1474815/run_schema.png"/>
</center>

Result: After the workflow 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.