Using Dendroscope

Aidan Budd


Getting Dendroscope

Dendroscope is a phylogenetic tree viewer. Thus, it is not designed to estimate trees, or to alter/edit the topologies of already-estimated trees.

The software can be downloaded from the University of Tuebingen, Germany, where it is developed. The software is available for all three major operating systems.

A manual for the software is available from this site.

Opening a File

There is more than one way to open a file
and then select file to be opened using you operating system's menus

File Format

Trees imported from other sources may need to be edited before they can be viewed in Dendroscope. For example, trees obtained from TreeFam contain comments provided in the form of text enclosed within square brackets i.e. [....]. Dendroscope cannot read trees containing comments in this form, so they should be removed before attempting to load such files into Dendroscope e.g. this is a tree downloaded from Treefam, here it is edited so it can be opened in Dendroscope.

Dendroscope Interface

The graphical user interface (GUI) for Dendroscope should look similar to the image shown below. The following components of the GUI are labeled


Displaying Taxa Labels - IMPORTANT!

To help present a large phylogeny in an uncluttered way, by default Dendroscope chooses to hide from view many of the taxa labels on a tree (where the labels would be overlapping and thus difficult to read) - this is controlled by the option:

View->Sparse Labels


However, if you are searching for a taxon-label corresponding to a particular sequence of interest, this can be problematic: the label you are looking for may have been hidden by Dendroscope.

Therefore, you will often want to switch off this option by simply selecting the View->Sparse Labels option (if there is a tick afer the option, then labels are being hidden)

Switching Between Different Tree Representations

There are two ways of doing this:
For example, the representation shown in the image above is obtained from Tree->Draw Rectangular Phylogram or from the Toolbar icon.

Selecting Branches/Nodes

Depending on the number of left mouse-clicks you give to a branch/node you can select
Mutliple branches/nodes/labels can be selected/deselcted by left mouse-clicking while holding the SHIFT key. The image below shows several branches, nodes, and labels highlighted.

Reroot Tree

Rotate Branches Around a Node

To rotate branches (which does not change the topology of the tree, only the way it is represented)

Formating Branches and Nodes

To change the colour/thickness/font etc. of selected nodes/branches/labels do:

Edit->Format

This brings up the "Format" window shown below


From here you can, for example:
See the image below for an example of such editing.

Adding Labels to Branches

It is possible to add text-labels to branches - for example to supply the name of a clade - e.g. vertebrates - associated with a particular group:
For example, the image below has a label added to the thick yellow branch.

Adjusting Positions of Labels

By simply left-clicking with the mouse and dragging it is possible to change the position of any of the labels (either branch labels as above, or the taxa labels at the end of branches. These labels remain attached to their branches and will move accordingly following rearrangements of the tree

Saving a Tree Representation

You can save the representation of your tree in a format that is read only by Dendroscope - this file can be reloaded into Dendroscope at a later date, and will have exactly the same set of rearrangements and formating as the trees in Dendroscope when the file was saved. You can do this using either of:
If you are looking to save the image for use in preparing a figure, then use

File->Export Image

and save the file in either EPS  or SVG format (to maintain it as a set of vectors rather than reducing it to a set of pixels as the other formats do)

The resulting file can then be loaded into a range of different software such as Adobe Illustrator to prepare a file version of a figure for publication/presentation

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