Tutorial - Evolutionary model inference (using ModelTest)
A view of the final workflow before execution.

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 this demonstration, we will use New_ModelTest as the project filename (as shown below). 

(Note: The new project file (New_ModelTest.db) will be created in the \projects\ directory).

Step 2. Insert a new alignment dataset

Go into the File Menu and select Import Alignment.

Select the file hiv.fasta located in the /examples directory using the file chooser dialog box (not shown).

After the selection, a new dialog box will be shown in which you can enter some informations about the sequences files, type of sequence (DNA, RNA, AA [amino acid]). Select the Import button when you''ll finished entering the sequence informations.

Once imported, you can find the newly imported multiple sequence alignment in the workflow Database panel.

(Note: The name of the Alignment might be different).

To use this multiple sequence alignment in your workflow, "drag and drop" it into the workflow area.

Step 3. Add jModelTest applications

Go into the Workflow Tools panel and using the same "drag and drop" motion, add the jModelTest application to the Workflow area.

Note: Select either jModelTest for nucleic acid data or ProtTest for amino acid data (proteins, peptides).

Now, to configure the evolutionnary model testing application (no configuration is required for ProtTest), open the  jModelTest configuration box by Double-Clicking with the Left Mouse button on the jModelTest application box and select in the Model selection the models that you want to test for this particular multiple sequence alignment.

For example, for this demonstration, we will include all the models (see the right panel) but leave the tree building and the statistic test to the default options.

Double-Click with the Left Mouse button on the red dot  (identifying the application data output) 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 yet.

Connect the alignment (examples\hiv.fasta) to the application box by selecting the connection box at the end of the alignment and linking it to the desired application.

Step 4. Execute the workflow

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

While the applications are running (or after they've produced the results), you can have access the application outputs by clicking on the Output panel.

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

Step 5. Display the results

The results will be in the results and outputText of the jModelTest application outputs. To access them, double-click on them.