Notung 2.6 is not the most recent version of Notung.  Notung 2.8   supports reconciliation with gene duplication, loss, horizontal transfer, and incomplete lineage sorting that supports phylogenomic analysis.

Description

Notung 2.6 is a software tool that offers a unified framework for incorporating duplication/loss parsimony into phylogenetic tasks, including

  • reconciling a gene tree with a species tree and estimating upper and lower bounds on the time of duplication;
  • rooting an unrooted gene tree by minimizing duplication and loss events;
  • rearranging a rooted gene tree in areas of weak sequence support to minimize the number of duplications and losses.
  • resolving a non-binary gene tree by fitting it to a binary species tree.

    All functions in Notung 2.6 (except resolution) are applicable to binary trees. In addition, Notung 2.6 can reconcile or root a non-binary gene tree with a binary species tree or a binary gene tree with a non-binary species tree. Notung 2.6 can also rearrange a non-binary gene tree with a binary species tree. Rearrangement of binary gene trees with non-binary species trees, and reconciliation, rooting, and rearrangement of of non-binary gene trees with non-binary species trees are currently open, algorithmic problems.

    These operations can be carried out via a graphical user interface that facilitates exploratory data analysis. Notung 2.6 also offers a command-line interface enabling the user to analyze a large number of gene trees automatically.

    Notung 2.6 was written by Benjamin Vernot, Aiton Goldman, Maureen Stolzer and Dannie Durand and is based on a novel algorithms for tree rearrangement [1] and non-binary reconciliation [1,2].   Notung is an extension of a program first presented by Chen, Durand and Farach-Colton [3]. The graphical user interface was constructed using the tree visualization library provided by FORESTER (version 1.92). [4].     For more information, contact mailto:notung@cs.cmu.edu

Citations

  [1]   A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction.
    D. Durand, B. V. Halldorsson, B. Vernot, 2005. Journal of Computational Biology, 13 (2): 320-335.
  [2]   Reconciliation with Non-Binary Species Trees
    B. Vernot, M. Stolzer, A. Goldman, D. Durand. 2007. Computational Systems Bioinformatics: CSB2007,
    Imperial College Press: 441-452
  [3]   Notung: A Program for Dating Gene Duplications and Optimizing Gene Family Trees.
    K. Chen, D. Durand, M.  Farach-Colton, 2000.     Journal of Computational Biology, 7 (3/4), 429-447.
  [4]   ATV: display and manipulation of annotated phylogenetic trees.
    C.M. Zmasek & S.R. Eddy, 2001. Bioinformatics, 17:383-384.