Notung offers a unified framework for incorporating duplication-loss parsimony into phylogenetic tasks. This parsimony principle asserts that gene duplication and gene loss are rare events. Notung’s functions embody the assumption that, in the absence of information from other sources, the phylogenetic hypothesis that requires the fewest duplications and losses to explain the data is preferred.
Notung can:
Notung differs from other reconciliation software in that it is the first and only software to reconcile and root non-binary gene trees with binary species trees and binary gene trees with non-binary species trees in addition to traditional analysis with binary gene trees and binary species trees. Another novel feature is Notung’s ability to rearrange and resolve non-binary gene trees.
The specific functions that Notung can perform on each combination of inputs are given in Table 1.1.
Gene Tree Species Tree Reconcile Root Rearrange Resolve Binary Binary yes yes yes N/A Non-Binary Binary yes yes yes yes Binary Non-Binary yes yes no N/A
Table 1.1: Notung’s main functions on binary and non-binary trees.
Notung provides a graphical interface for tree manipulation and visualization and offers a command line option that can be used for automated analysis of a large number of trees.
Notung utilizes novel, efficient algorithms [1, 3, 16] for reconstructing the history of gene duplications and losses, for rooting gene trees based on duplication/loss parsimony and for the rearrangement of weakly supported areas of gene trees.
More information about Notung can be found at:
More information about other Durand Lab projects can be found at:
Notung can be used to address a broad range of applications. It can assist scientists who wish to bring gene duplication models to bear on gene tree construction; evolutionary biologists studying the history of a gene family; and experimental biologists interested in incorporating evolutionary insights into questions of function and structure.
The graphical user interface was partially constructed using the tree visualization library provided by FORESTER (version 1.92) [17].
NOTE: While other events besides duplication and loss, such as horizontal gene transfer, may be the cause of gene tree-species tree disagreement, Notung does not consider these other events.
D. Durand, B. V. Halldorsson, B. Vernot. A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. Journal of Computational Biology, 13(2):320-335, 2006.
B. Vernot, M. Stolzer, A. Goldman, and D. Durand. Reconciliation with non-binary species trees. Journal of Computational Biology, in press, 2008. Also appeared in Computational Systems Bioinformatics: CSB2007 Conference Proceedings, Imperial College Press: 441-452.
This manual provides a detailed description of Notung, and gives step-by-step instructions for Notung’s tasks and visualization features. It assumes familiarity with basic concepts of phylogeny reconstruction. For more information on these subjects, refer to basic textbooks, such as [4, 11]. A Glossary is provided. Additional sources are provided in the Bibliography.
The manual is organized into numbered chapters by topic. Each chapter begins with paragraphs describing the topic, followed by a list of step-by-step commands for operations associated with the topic. Figures showing the Notung graphical user interface (GUI) have been included to illustrate program displays and command results.
Instructions for downloading Notung for various operating systems is provided in Chapter 2. A basic introduction to the Notung GUI is provided in Chapter 3. A brief discussion regarding the relevant evolutionary theories regarding non-binary species and gene trees will be provided in Chapter 4. Notung’s six task modes are described in Chapter 5 - Chapter 10. Chapter 11 discusses the options for changing the appearance of the tree. Detailed information regarding batch processing of trees using the command line is located in Chapter 12. More detailed information about input/output and tree file formats are given in the Appendix A.