Notung-2.9 is a gene tree-species tree reconciliation software package that supports duplication-loss (DL) and duplication-transfer-loss (DTL) event models with a parsimony-based optimization criterion.

     Please go to Notung-DM for our new reconciliation engine that infers domain events during the evolution of multidomain protein families.

New in 2.9:

  • Homology inference: Identifies all pairs of orthologs, paralogs and xenologs in a reconciled gene tree. Xenologs are further assigned to subclasses based on the homology framework described in Xenolog Classification [1].
  • Phylogenomics: Notung's --phylogenomics command line option aggregates results across all reconciled gene trees and generates summary reports of
    • 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.
  • Performance upgrade:
    • Streamlined code for reconciliation.
    • Implemented memoization for temporal feasibility. This reduces the runtime by 5 fold.
    • Updated deprecated functions within java runtime.

The Notung platform

Degeneracy and feasibility: With a duplication-transfer-loss (DTL) event model, there may be more than one minimum-cost event history that reconciles the gene and species trees. Transfers imply temporal constraints because the donor and recipient of a transfer must have co-existed; a reconciliation is feasible if all temporal constraints are mutually compatible. Notung-2.9 reports all optimal reconciliations that are temporally feasible, up to a user-specified limit.

Species-tree aware functions: Notung-2.9 offers a unified framework for incorporating event parsimony into phylogenetic tasks, including rooting an unrooted gene tree, rearranging of a rooted gene tree in areas of weak sequence support, and resolving a non-binary gene tree.

Unresolved trees: Most tasks can be performed with an unresolved (non-binary) gene or species tree. Notung's model of reconciliation with a non-binary species tree avoids overestimating duplications in gene trees that are incongruent due to incomplete lineage sorting.

User interface: Notung-2.9 offers a graphical user interface that facilitates exploratory data analysis, as well as a command-line interface that supports analysis of a large number of gene trees automatically.

For more information, contact notung@cs.cmu.edu

     Notung was written by Maureen Stolzer, Han Lai, Benjamin Vernot, Charlotte Darby, Minli Xu, Aiton Goldman, Deepa Sathaye, and Dannie Durand and is based on novel algorithms for xenolog classification [1], DTLI-model reconciliation [2], tree rearrangement [3], and non-binary reconciliation [3,4].   Notung is an extension of a program first presented by Chen, Durand and Farach-Colton [5]. The graphical user interface was constructed using the tree visualization library provided by FORESTER (version 1.92) [6].

Citations

  [1]   Xenolog Classification.
    C. Darby, M. Stolzer, P. Ropp, D. Barker, D. Durand, 2017. Bioinformatics, in press.
  [2]   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.
  [3]   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.
  [4]   Reconciliation with Non-Binary Species Trees
    B. Vernot, M. Stolzer, A. Goldman, D. Durand, 2008. Journal of Computational Biology, 15(8): 981-1006.
  [5]   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.
  [6]   ATV: display and manipulation of annotated phylogenetic trees.
    C.M. Zmasek & S.R. Eddy, 2001. Bioinformatics, 17:383-384.

The phylogenetic data used in Darby et al. are available through the Edinburgh Datashare. These trees are stored in perpetuity with the DOI 10.7488/ds/1503 and are publicly available, free of charge, under a Creative Commons license.

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.