This page specifically describes the Notung applet associated with the P-POD website. General information and documentation for Notung can be found here: http://www.cs.cmu.edu/~durand/Notung.

About Notung

The Notung program offers a unified framework for incorporating duplication-loss parsimony into a into broad range of phylogenetic tasks. Notung infers orthology, gene duplication, and gene loss by comparing a gene tree to a known species tree. Other functions include rooting a tree, correcting errors in trees based on weak sequence evidence, estimating bounds on the time of duplication, and visualizing gene duplications, losses, paralogs and orthologs.

Investigating P-POD families with the Notung applet

P-POD users can further explore P-POD families with the Notung applet, which is included in the P-POD website, allowing users to analyze P-POD trees directly without downloading trees or software. The applet provides a subset of the functions offered by the full Notung stand-alone program, which is freely available. In particular, the Notung applet can be used to:

Interactively view the gene tree, and the associated species tree, for any P-POD family.
Visually explore ortholog and paralog relationships in P-POD gene families.
View information about alternate rootings and reroot a P-POD family tree on a different branch.
Consider alternate arrangements of short branches (i.e., branches that are only weakly supported by the sequence evidence) in P-POD trees.

Some of Notung's functions (primarily I/O related functions) are not provided by the applet, due to general limitations on the functions that applets can perform. Users wishing to use the full range of Notung functions can carry out further analyses on their local computers by downloading P-POD trees and the Notung stand-alone program (see below).

Functions that are not available in the Notung applet, but can be performed by the stand-alone program, include:

Save a tree that has been modified in Notung.
Save PNG images of trees that have been modified in Notung.
Open other trees (e.g., gene trees stored on your local computer or available through another website) in Notung.

Here are some ways to work around the applet's I/O limitations:

Saving a tree that has a been modified in Notung: A text representation of the tree currently being viewed in Notung can be obtained in a popup window using File » View Tree in Text format. This text can then be saved by copying and pasting it to a file. More information about the tree file formats used by Notung is available at add link, or via File » View Tree in Text format » About Tree Formats. If you have modified a tree in the Notung applet, and wish to reopen this tree in the stand-alone version of Notung, save it in Notung format. If you wish to reopen your modified tree in another tree program, Newick format may be a better option.
Images of trees modified in Notung can be obtained directly from the applet by obtaining a screenshot of the applet and inserting it into an image editor, Powerpoint, or other suitable program. The best way to take a screenshot will depend on your local computing environment and the operating system you are running. Contact your local technical support organization for advice.
Download the Notung stand-alone application and perform your analysis locally. The stand-alone application offers a full range of I/O functions, including opening new trees, saving trees, and saving tree images in PNG file format for use in publications, web pages, etc.

Downloading Notung and P-POD Trees

To download a P-POD family tree directly from the P-POD website click on the "Download Files" link available on the P-POD family display.

The Notung stand-alone application is freely available and runs on all platforms with Java version 1.4.2 or greater. If P-POD users wish to take advantage of its full range of functions, Notung can be downloaded from the Notung website, http://www.cs.cmu.edu/~durand/Notung. A full description of Notung's functions is given at: http://goby.compbio.cs.cmu.edu/Notung/documentation.