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:

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:

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

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/2.6_documentation.html.