- Evolutionary model inference (using ModelTest)A view of the final workflow before execution.
5 steps required
Step 1. Open a new
Open the File Menu
When asked if you want to migrate your data and workflow to the new
project, select NO
Then enter a new project
For this demonstration, we will use New_ModelTest
as the project filename (as shown below
The new project
file (New_ModelTest.db) will be created in the \projects\
Step 2. Insert a new alignment dataset
Go into the File Menu
Select the file hiv.fasta
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
(Note: The name of the Alignment might be different).
To use this multiple sequence alignment in your workflow, "drag and
it into the workflow
Step 3. Add jModelTest applications
Go into the Workflow Tools
and using the same "drag and drop
" motion, add the jModelTest
application to the Workflow
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
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
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
While the applications are running (or
after they've produced the results
), you can have access the application outputs
by clicking on the Output
(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