Notung 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.
Click here for Notung-3.0 BETA pre-release version of our next major release.
Click here for Notung-2.9 , the most recent version of our current release
Click here for Notung-DM for our new reconciliation engine that infers domain events during the evolution of multidomain protein families.
The Notung 2.9 platform
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 .
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 .
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 phylogenomic functions have been further extended in Notung-3.0
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 [2, 3]
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.
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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 , DTLI-model reconciliation , tree rearrangement  and non-binary reconciliation [2, 3]. Notung is an extension of a program first presented by Chen, Durand and Farach-Colton . The graphical user interface was constructed using the tree visualization library provided by FORESTER (version 1.92) .
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.