DrPhylo: Assessing Clade Fragility

The DrPhylo analysis requires a rooted tree and sequence alignment data for each gene or domain of interest. This tutorial will show how to run the DrPhylo analysis using Fungi example data that is provided with MEGA’s installer.

On the bottom toolbar of the main form, click the Examples button. With the Examples folder open, navigate to the DrPhylo sub-folder and select the Rooted_Fungi_Tree.nwk file (if this file is not visible, set the filter to All Files)
The tree of Fungi will be displayed in the Tree Explorer window. Right-click the branch for the Saccharomyces clade and select Launch DrPhylo from the context-menu.

In the DrPhylo Settings window that is displayed, click the Use FASTA Files From Directory radio button and then click the folder icon. In the Select Folder window that is displayed, select the ~/Documents/Examples/DrPhylo/alignments folder that is included with the MEGA installation. This directory contains aligned FASTA files for each gene of interest.
Under Character Types to Encode, click the Protein check box.
Click the OK button to launch the analysis.

Progress will be displayed while the analysis runs and when it is finished, MEGA will display the DrPhylo Model Grid. The Model Grid shows the most influential genes in each species as well as the species classification probability (in parentheses) for each species in the clade tested.

In addition to the Model Grid, DrPhylo produces various results files that can be accessed from the main form by clicking on the DrP icon. To save the results to you local file system, click the DrP icon on main form and click the Save Results to File System... menu item.

Besides using a directory of FASTA alignment files for the genes/domains to be analyzed, a sequence alignment that is active in MEGA can be used. If genes and domains are defined for the active alignment, then DrPhylo can be run such that MEGA will generate a separate FASTA file for each gene or domain. Alternatively, the active data can be partitioned into segments that encompass a set number of positions in the alignment and FASTA files generated for each partition and then analyzed by DrPhylo.

A quick example is to use the Chloroplast_Martin.meg alignment file that is included in the MEGA installer:

On the main form, click the Examples button on the bottom toolbar and select the Chloroplast_Martin.meg file to activate it.
To quickly see the genes that are defined in this file, on the main form click Data->Select Genes/Domains... The Genes/Domains window will be displayed with the names and bounds for the genes and domains defined in the alignment file. Click the OK button to close this window.

On the main form, click Phylogeny->Construct/Test Neighbor-Joining Tree...
In the Analysis Preferences Dialog, click the OK button to launch the tree construction analysis.
The results will be displayed in the Tree Explorer window. In this window, right-click a branch in the tree and select Launch DrPhylo from the context menu.
In the DrPhylo Settings window, click the Use Defined Genes/Domains of Active Data radio button.
Click the OK button to launch the analysis. DrPhylo will run the analysis gene by gene and display the results
Alternatively, the option to Partition Active Data can be chosen in the DrPhylo Settings window.