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:
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.
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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 [3,4]. 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.