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.
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
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).
- 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
- 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
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:
- 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.
- 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
- 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/2.6_documentation.html.