Appendix G Notung as an Applet
In addition to a stand-alone application, Notung is available as a Java applet that can be embedded in an HTML page and executed in any java-enabled web browser. You can use the Notung applet to present phylogenetic data on the web, by creating a webpage that allows visitors to your site to view, analyze or manipulate trees interactively using Notung.
Section G.1 is intended for Notung applet users. It describes the Notung applet functions and user interface, focusing primarily on differences between the applet and the standalone application. Section Section G.2 is targeted at web site developers and describes how to embed the Notung applet in an HTML file.
Problem Possible Causes Solutions When I tried to reconcile the trees, I received this error message: “None of the species labels in this tree can be found in the species tree. Try checking your reconciliation settings.”
- The species labels in the gene tree leaf node names are not compatible with the species labels in the species tree.
- The “Specify Species Label” setting in the Reconciliation Options dialog box has been set incorrectly.
- The incorrect species tree has been selected for reconciliation.
- Check the species labels in the gene tree to make sure they match the species labels in the species tree.
- In the Reconciliation Options dialog, make sure you select the appropriate naming convention for species labels.
- In the Reconciliation Options dialog, make sure you select the appropriate species tree for reconciliation.
The edge weights on the gene tree are not what you expected. Notung has mistaken the branch length values in the Newick file for edge weight values. See Appendix A.6 - Location of Edge Weight Values First, open the gene tree file in a text editor to determine the location of edge weight values. Then, click “Display Options → Select Location of Edge Weights” and set the location of Edge Weights appropriately. My gene tree should have edge weights, but when I load the tree, weights are not displayed on some branches. The gene tree file is supposed to be in Newick, NHX or Notung format, but contains a typo or formatting error, affecting the edge weight location. Open the original tree file in a tree editing program or text editor and correct any formatting errors. NOTE: Some formats are case-sensitive. When I tried to reconcile the gene tree with the species tree, I received this message: “There are no species trees to reconcile with.” -or- My species tree is not listed in the drop down menu in the Reconciliation Options dialog box. You have opened a species tree as a gene tree. Reopen the desired species tree as a species tree using “File → Open Species Tree” or “Ctrl-Shift-O”. After reconciliation, I found lost genes in unrecognizable species, such as “n101.” The gene was lost in an ancestral species that was not given a label in the original species tree file. When internal node names are not specified in the input file, Notung generates them using an arbitrary counting system (ex: n101). Use “Display Options → Display Internal Node Names” to examine internal species names in the species tree. If you prefer taxonomic names, use a tree editing program or text editor to add real species names to internal nodes in the species tree. When I tried to open a tree, I received this message: “An error occurred while opening your file. Please check the format.” Or “An error occurred while opening your file. Node had malformed information.”
- The gene tree file is supposed to be in Newick, NHX or Notung format, but contains a typo or formatting error.
- The gene tree file is in a format Notung does not accept, (ex: Nexus).
- Open the original tree file in a tree editing program or text editor and correct any formatting errors.
- Convert the file to Newick or NXH file format. See Appendix A - File Formats for more information about file formats.
Notung reports that you do not have a recent enough version of Java, but you have the latest version installed. You have multiple versions of Java installed.
- On Windows, bring up the properties window for the Notung-2.6 jar file. Check the “Opens With” field - if the wrong version of java is listed, change it so that the right version of java is being used.
- On Linux, type java -version - this will tell you which version of Java is being used. If it is incorrect, alter your path environment variable to include the proper version of Java.
The species tree file I created using the NCBI Taxonomy Browser contained non-ASCII characters. As part of its file construction, the NCBI Taxonomy Browser includes some non-ASCII characters. These characters are ignored by Notung, but you can open the tree file in a text editor and delete the non-ASCII characters. The species tree file I created using the NCBI Taxonomy Browser contained 4’s. As part of its file construction, the NCBI Taxonomy Browser includes a branch length of 4 for every edge in the species trees it produces. These branch lengths are ignored by Notung, but you can open the tree file in a tree editing program or text editor and delete the branch lengths. The names of internal nodes in my gene tree change over time.
- The gene tree file does not specify internal node names and has been reloaded. When internal node names are not specified in the input file, Notung generates them using an arbitrary counting system (ex: n101).
- Node names were given in the original tree file, but additional nodes have been added, because either rearrangement or resolve has been performed. Added nodes are assigned names that begin with an ‘r’ and are followed by numbers (ex: r245).
- If you want the internal node names to be the same every time the tree is opened, use a tree editing program or text editor to add names to internal nodes in the gene tree.
- Notung cannot track internal nodes that are temporary or not present in the original file. If you need permanent names for these nodes, save the file and use a tree editing program or text editor to specify names for these nodes.
I use the <Tab> key to navigate to a different button in a popup box, but when I hit the <Enter> key, the selected button is not engaged. This is a problem with some versions of Java. The <Tab> key option to navigate to different buttons does not select the “highlighted” button. When the <Enter> key is pressed, the originally selected button is used. Use the mouse to select buttons in the windows I have added a node to an annotation, but the node does not appear in the correct color. There are conflicting annotations - the node corresponds to more than one annotation and is currently being described by another annotation. Annotations have precedence - those annotations added later will always take precedence over earlier annotations. Manually remove the node from the other annotations, or check the other annotations and remove any search strings that identify the node of interest. See Chapter 10 - Annotations for more information.