Appendix B  Building a Species Tree

Most functions in Notung require a species tree. If you are familiar with the species in your data set, you may already have an appropriate species tree. If you do not have one, you can construct one using resources available on the web.

One such resource is the NCBI Taxonomy Browser, available at the NCBI website:

http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi

The Taxonomy Browser contains a database of all organisms represented in the NCBI sequence database, and can automatically build a species tree using species selected by the user. To create a tree in a format Notung can understand, add the species to be included in the tree, and then use the Taxonomy Browser’s “Save As” option to save the tree as a Phylip tree. The Phylip option causes the tree to be saved in a variant of Newick format. The resulting tree can then be loaded into Notung as a species tree.

NOTE: The Taxonomy Browser does not recognize all common species names. Formal names for species can be found at:

http://www.expasy.org/cgi-bin/speclist

To build a species tree using the NCBI Taxonomy Browser:

1. Go to: http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi.
2. In the text field labeled “Enter name or id,” enter the Latin name or common name of the species to add to the tree.
3. Click “Add.” If the taxonomy browser did not recognize the species name, a pink error bar which reads “Organism name ’name’ not found” will appear.
4. When you have finished adding species, find the pull-down menu that says “text tree.” Drag down and select “phylip tree.”
5. Click “Save As, and save the species tree.”

Additional resources provide access to existing species trees built by other researchers. TreeBASE (http://www.treebase.org/treebase/search.html) allows users to search for species trees from a large database of published papers. The Angiosperm Phylogeny Website and the Phylomatic Project provide species trees for plant species.

http://www.mobot.org/MOBOT/research/APweb/welcome.html

http://www.phylodiversity.net/phylomatic/phylomatic.html

Other tree-building tools are listed on Felsenstein’s Phylogeny Programs website:

http://evolution.genetics.washington.edu/phylip/software.html.

NOTE:

• Species trees obtained from the Taxonomy Browser and other resources will not necessarily be bifurcating. To correct this, you can either edit the tree file in a text editor or tree editor or use the non-binary species tree with a binary gene tree. See Chapter 4 - Non-Binary Trees for more information.
• The Phylip tree files generated by the Taxonomy Browser contain non-ASCII characters and have branch lengths of four within the tree, but these characters have no effect on the tree when it is opened in Notung.