Notung 2.8 does transfers!   Notung 2.8 does phylogenomics!

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Notung 2.8 is a reconciliation engine for the Duplication, Transfer, Loss, Incomplete Lineage Sorting (DTLI) model [1] that supports phylogenomic analysis. Notung's new phylogenomics option supports integrated analysis of large collections of gene families drawn from a set of genomes. In addition to reporting the events inferred for individual trees, this function aggregates and summarizes results across all reconciled gene trees and all nodes or branches of the species tree:

  • gene origin: the species in which each gene family first appeared;
  • ancestral gene content: gene family copy number in each ancestral species;
  • timing of events: the number of duplications, losses, and transfers that occurred in each species.

The integrated results from all reconciled gene families supports stratigraphic analysis of gene age relative to the species tree, co-evolution of gene families with related function, and investigation of genome-scale evolutionary trends, such as whole genome duplications, bursts of lateral transfer activity, and massive loss characteristic of genome reduction.

    Notung was written by Benjamin Vernot, Aiton Goldman, Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, and Dannie Durand and is based on novel algorithms for DTLI-model reconciliation [1], tree rearrangement [2] and non-binary reconciliation [2,3].   Notung is an extension of a program first presented by Chen, Durand and Farach-Colton [4]. The graphical user interface was constructed using the tree visualization library provided by FORESTER (version 1.92). [5].     For more information, contact mailto:notung@cs.cmu.edu

Citations

  [1]   A Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary
   species trees. M. Stolzer, H. Lai, M. Xu, D. Sathaye, B. Vernot, D. Durand, 2012. Bioinformatics, 28 (18): i409-i415.
  [2]   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.
  [3]   Reconciliation with Non-Binary Species Trees
    B. Vernot, M. Stolzer, A. Goldman, D. Durand. 2007. Computational Systems Bioinformatics: CSB2007,
    Imperial College Press: 441-452
  [4]   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.
  [5]   ATV: display and manipulation of annotated phylogenetic trees.
    C.M. Zmasek & S.R. Eddy, 2001. Bioinformatics, 17:383-384.


This work was supported in part by NSF Grant DBI1262593.   Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.