Also check out Notung 2.7 Beta :   reconciliation with gene duplication, gene loss, horizontal gene transfer, incomplete lineage sorting.

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 of Notung 2.6's functions (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.