Contents
Chapter 1 Introduction to Notung
1.1 How to cite Notung
1.2 Using This Manual
Chapter 2 Downloading Notung
Chapter 3 Getting Started
3.1 Gene and Species Trees
3.2 The Graphical User Interface
3.3 File Menu & Opening and Saving Trees
3.4 General Tree Statistics
3.5 Parameter Values
Chapter 4 Non-Binary Trees
4.1 Non-Binary Trees
4.2 Fitting Binary Gene Trees to Non-Binary Species Trees
4.3 Fitting a Non-Binary Gene Tree to a Binary Species Tree
Chapter 5 Reconciliation Mode
5.1 Reconciling Non-Binary Trees
5.2 Using Reconciliation Commands
5.3 Inferring Orthologs and Paralogs
Chapter 6 Rooting Mode
Chapter 7 Rearrange Mode
7.1 Alternate Optimal Hypotheses
7.2 Rearrangement Commands
Chapter 8 Resolve Mode
Chapter 9 History
Chapter 10 Annotations
Chapter 11 Changing the Appearance of the Tree Panel
11.1 Display Options
11.2 Zoom
11.3 Changing Font Size
Chapter 12 Command Line Options and Batch Processing
12.1 Opening and Using a Command Window/Terminal
12.2 Running Notung from the command line
12.3 Running Notung from a Batch File
12.4 Saving PNG Images of Trees
12.5 Options for Reconciling with Non-Binary Trees
Appendix A File Formats
A.1 Newick File Format
A.2 NHX File Format - New Hampshire eXtended
A.3 Notung File Format
A.4 Specifying the Species Associated with Each Gene
A.5 Punctuation in Species Names
A.6 Location of Edge Weight Values
Appendix B Building a Species Tree
Appendix C Glossary
Appendix D Keystroke Shortcuts
Appendix E Worked Examples
E.1 Exercise 1 - Reconciling a gene tree with a species tree
E.2 Exercise 2 - Rooting an unrooted tree
E.3 Exercise 3 - Rearranging a gene tree
E.4 Exercise 4 - Binary gene tree with a non-binary species tree
E.5 Exercise 5 - Non-binary gene tree with a binary species tree
Appendix F Troubleshooting
Appendix G Notung as an Applet
G.1 Using the Notung Applet
G.2 Setting up the Notung applet