NOTUNG

Owned by Sheldon McKay
Last updated: Aug 26, 2009Version comment

Prepared by: phtully

Tool Name: NOTUNG

Homepage: http://www.cs.cmu.edu/~durand/Notung/

Platforms: Mac OS X, Linux, Windows

Implementation Language: Java

Mailing List: Yes

Documentation/Manual: http://goby.compbio.cs.cmu.edu/Notung/2.6_documentation.html

Purpose:
Gene tree reconstruction or post hoc analysis of any rooted tree (with bootstrap values) for alternative hypothesis evaluation.

Description:
NOTUNG is reconstruction software that seeks to minimize gene duplication and gene loss events in both binary and non-binary phylogenetic trees. Operation under the principle of duplication-loss parsimony is duly noted. Functional modes are implemented within a GUI environment to allow for data visualization:

  • Reconciliation Mode: inference of gene duplication and loss by comparison of compatible gene/species trees. Displays loss statistics, infers orthologous and paralogous relationships, and determines lower and upper bounds on the time of each duplication.
  • Rooting Mode: root inference by calculation of a root score for each edge in the gene tree followed by explicit designation of the root.
  • Rearrange Mode: reorganization of weakly-supported edge regions to produce an alternate event history with the lowest D/L score.
  • Resolve Mode: all of the polytomies (node degree > 3) in the original non-binary gene tree are removed and replaced with new edges to produce a new binary tree with optimal D/L score.

Inputs:

Gene Family and Species trees (see below for formats) with bootstrap (edge weight) thresholds

  • Newick
  • NHX
  • Notung

Outputs:

  • text representation of trees in any of the aforementioned input formats
  • text summary of gene duplication history, including list of duplication nodes with bounds on time of duplication for each one
  • tree image (.png)
  • ortholog/paralog table (HTML, CSV, tab-delimited)

Relevant Publications:

Chen, K., Durand, D. and M. Farach-Colton. 2000. NOTUNG: a program for dating gene duplications and optimizing gene family trees. Journal of Computational Biology 7(3-4): 429-447.

Stolzer, M., Goldman, A. and Durand, D. 2007. Reconciliation with non-binary species trees. Computational Systems Bioinformatics: CSB2007 Conference Proceedings, Imperial College Press, 2007: 441-442

Durand, D., B. V. Halldorsson, and B. Vernot. 2005. A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. Journal of Computational Biology 13(2): 320-335.

Related Software:

  • Forester
  • COMPONENT
  • GENETREE
  • FamFetch

Defining Characteristics:
Ability to handle non-binary trees, GUI interface for visualiazation, large scale snalysis using rooted and unrooted trees.

Comparison with other Phylogeny based Tools (use of Gene/Species tree comparison):

  • Tool UREC (Unrooted REConciliation) is more efficient (source) but is only available via command line interface. The intricacies of the algorithmic methodology implemented in NOTUNG are unclear especially when it comes to how the distribution of costs assigned to the nodes of a reconciled tree look when there are two or more optimal rootings (source).
  • Tool SoftParsMap allows both gene and species treees to be unresolved whereas NOTUNG requires species tree to be resolved . But this tool is also availale only via command line, and the input format requirements are less straightforward than in NOTUNG.

Performance/Scalability:
Published analyses of NOTUNG performance: Reconciliation with NonBinary species trees (page 10),