Notung 2.6 : A Manual
Dave Danicic, Dannie Durand, Aiton Goldman,
Maureen Stolzer, Benjamin Vernot
Contents
Introduction to Notung
How to cite Notung
Using This Manual
Downloading Notung
Getting Started
Gene and Species Trees
The Graphical User Interface
File Menu & Opening and Saving Trees
General Tree Statistics
Parameter Values
Non-Binary Trees
Non-Binary Trees
Fitting Binary Gene Trees to Non-Binary Species Trees
Fitting a Non-Binary Gene Tree to a Binary Species Tree
Reconciliation Mode
Reconciling Non-Binary Trees
Using Reconciliation Commands
Inferring Orthologs and Paralogs
Rooting Mode
Rearrange Mode
Alternate Optimal Hypotheses
Rearrangement Commands
Resolve Mode
History
Annotations
Changing the Appearance of the Tree Panel
Display Options
Zoom
Changing Font Size
Command Line Options and Batch Processing
Opening and Using a Command Window/Terminal
Running Notung from the command line
Running Notung from a Batch File
Saving PNG Images of Trees
Options for Reconciling with Non-Binary Trees
File Formats
Newick File Format
NHX File Format - New Hampshire eXtended
Notung File Format
Specifying the Species Associated with Each Gene
Punctuation in Species Names
Location of Edge Weight Values
Building a Species Tree
Glossary
Keystroke Shortcuts
Worked Examples
Exercise 1 - Reconciling a gene tree with a species tree
Exercise 2 - Rooting an unrooted tree
Exercise 3 - Rearranging a gene tree
Exercise 4 - Binary gene tree with a non-binary species tree
Exercise 5 - Non-binary gene tree with a binary species tree
Troubleshooting
Using the Notung Applet
Notung as an Applet
Setting up the Notung applet
References
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