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.
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) .
This work was supported in part by NSF Grant DBI-1262593. 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.