Tutorial - Multiple Sequence Alignment (MSA) with ClustalW2 and Muscle
The final workflow after the execution and some results.

5 steps required
Step 1. Open a new workflow project

Open the File Menu and select New.

When asked if you want to migrate your data and workflow to the new project, select NO.

Then, enter a new project filename. For the time being, we will be working with the default name. 
The new project file (New_Untitled.db) will be in the \projects\ directory.

Step 2. Insert a new sequence dataset

Go into the File Menu and select the Import Sequences menu.

Select the file hiv.fasta located in the /examples directory.

A new dialog box will be shown where you can enter some informations about the sequence files, type of sequences (DNA, RNA or AA [Amino Acid]).
Select import when you''ve finished entering informations.

Note: The name prefix will be added to all files. It allows for a simplified loading of multiple sequence alignment files.

Once imported, you can find the newly imported MultipleSequences in the Workflow Database pane. (Note: the name of the MultipleSequences might be different).

To use it, "drag and drop" the new MultipleSequences object into the Workflow area (see below).

Step 3. Add the MSA applications

Go into the Workflow Tools Pane and using the same "drag and drop" motion, add the ClustalW and Muscle application to the Workflow area.

Note: Executing this workflow locally can be SLOW. If you have Internet access, you can use the ClustalW2 (Web EBI) and Muscle (Web EBI) applications instead, which result in a running time of ~7 minutes for this HIV dataset.

To speed up the analysis, open the Muscle configuration box by Double-Clicking with the left mouse button on the Muscle application box and select in the "Fast setting" the "Fastest possible (nucleotides)".

Double-Click with the left mouse button on the Red dot  (identifying the application data outputs) to show all application outputs.

Note: The blue color for any input or output data indicates that either it is undefined or has not been generated.  Once the data are genetated, the output will turn to the green color, as shown below.

Connect the MultipleSequences (examples\hiv.fasta) to the applications box by selecting the connection box at the end of  the MultipleSequences object and link it to each of the multiple sequence alignment applications (i.e. ClustalW2 and Muscle).

Step 4. Execute the workflow

In the far right corner of the worflow artea, click on the Run button.

While the applications are running you can see the application progress either by looking at the workflow progress bar (above the workflow area) or by  clicking on the Output panel (see below).

You can save this generated application output to a text file by clicking on the bottom-left button "Save as Text".

When all the workflow executions have been carried out, a should appear on the right-corner of each application box. If an error has occured, a warning sign will be displayed.

Step 5. Display the results

To view a Text View of the multiple sequence alignment, either double-click on the application aligment output or right-click on it and select "View".

In this view (see below), you can select either a simplified representation of the aligned sequences, or a fasta or phylip format for rapid "Cut-and-Paste" to other applications.

To display a more graphic representations,  right-click on the aligment output and select "View Graphic".