PSODA Tutorial

6/27/2009

PSODA provides alignment, phylogenetic search and selection detection for sequence data. This tutorial will provide usage examples to help with the details of performing a PSODA sequence data analysis.

Getting Started

When you first start the PSODA application you will see a panel asking you to register. We will send email to the address provided when new versions are available. You will only have to register once in order to use the application.

Once you have registered, you will see a screen with references for major components of the system. If you use these systems for your data analysis, you can reference these papers to give credit to the authors. Jalview, mrbayes, RAxML, treesaap are all incorporated into PSODA. This tutorial will show you how to use these tools as well as native PSODA functionality.

Opening Files

The File menu in the upper left of the application can be used to open files containing data and commands. Two formats are recognized by PSODA:

• Aligned sequence data Nexus format files are similar to Paup* and many Paup* commands are availalable in PSODA. To perform an analysis using a nexus file, select the File menu and select the "File Format" box to show "NEXUS files".
• Unaligned fasta format files can also be opened with PSODA. Select the FASTA File Format and navigate to the desired file.
• If the data file has another format, the "Open in Data Convert" option to convert files with various other formats.

For this tutorial, open the "alignHIV.fasta" file.

Once the sequence file has been opened, it will appear in the "File Editor windotab at the top of the PSODA window. Changes can be made to the sequence data in this window, but the file must be saved before further processing can occur.

Performing Analyses

Most of the processing in PSODA occurs in the PSODA tab. You can switch between operations by selecting this tab.

Performing Manual Analyses

If the current file is a fasta raw sequence file, select the "Run " button to load the data into PSODA. All operations available in the "Commands" menu at the bottom of the window will be applied to the current dataset loaded into the system.

Aligning Data

Fasta data must be aligned before phylogenetic analysis can be performed. Select the align command from the "Commands" menu and the alignment options window will appear.

Default values are populated for the command, and these values can be changed depending on the user preference. A full description of the options can be found in the user manual, or by running the "help" command with "align" as the "name". Select the "Run align" button to perform the alignment.

Feedback from the align command is provided in the PSODA window. When the command is complete, further processing can occur.

Visualizing the Alignmenet

Jalview has been included with PSODA in order to provide an alignment viewer. Select the "Export to Jalview" button to view the alignment of the current dataset.

Jalview can also be used to perform MAFFT or MUSCLE alignments throgh external servers using the "Web Service" tab. Notice that the tab bar on the top of the window was changed to Jalview. To execute further commands, select the "PSODA" tab.

Performing a Phylogenetic Search

The "hsearch" command performs a heuristic TBR search for a phylogenetic tree given aligned data. Select the "hsearch" command and the corresponding options box will appear.

Parsimony or Likelihood searches can be selected and the start tree can be the current tree or a stepwise tree. For now, run the command with the defaults. The Interaction window will show the progress of the search. When the search is complete, the resulting trees can be displayed in the "Trees" pane at the bottom of the window.

Double clicking on the tree will bring up ATV, which will allow you to view the selected tree.

Performing a Selection Analysis

With a phylogenetic tree, selection analysis using treesaap can be performed. Click on the "Export to Treesaap" button to start selection detection. A description of the treesaap options can be found in the treesaap manual, but for now, just click on the "Run" button in the bottom right corner of the window.

This comand may take several minutes, but eventually a progress bar should appear.

The "Summary" window will show which chemical properties are under selection with "0.05", "0.01", and "0.001" P values.

By selecting the "Sequence Analysis" tab at the top of the "Results" window, selection for different chemical properties can be visualized across columns in the alignment.

Running a Command File

A nexus file can also contain commands that will automatically be run when the file is loaded. These commands are listed in the PAUP or PSODA block after the sequence data. Commands that can be entered from the "Commands" menu can also be entered into a nexus file for automated processing. Open the "4taxa.nex" file for an example of this approach, go to the PSODA tab and run the file.

This concludes the tutorial. Consult the user manual for a description of other options used in PSODA.