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

File->Open
Use the "Open Tree File" icon

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

the Main Window - where the phylogeny/tree is viewed
the Menu Bar - providing a range of different options to mainpulate the view of the phylogeny
the Side Bar - provides a list of all the trees present in the current file
the Toolbar - provides short-cuts to several of the more commonly-used menu items
Context Menus - right mouse-click on different regions of the screen to obtain additional options applied to the selected region

nodes
edges
background (allows selection of all edges/nodes/labels)

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:

Choosing the appropriate "Tree Representation" icon from the toolbar
Use the Tree menu

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

one click - only the clicked-on branch
two clicks - the entire clade associated with one end of the branch (including branches, nodes, and labels)
three clicks - the entire clade associated with the other end of the branch (including branches, nodes, and labels)

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

Left-click with the mouse on the branch you want to rotate around to select it and then either:

Select the "Reroot tree" Toolbar icon
Edit->Reroot

Rotate Branches Around a Node

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

Left-click with the mouse on the node you want to rotate around to select it and then either:

Select the "Swap order of subtrees below node" Toolbar icon
Edit->Swap Subtree
Right-click to obtain the node Context Menu and choose "Swap Subtree"

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:

change the width of branches by altering the "Edge Width"
change the colour of the selected nodes/branches/labels by clicking on the colour pallet to choose the appropriate colour
change the size of the text used for the labels using the middle-top menu-box (above this contains the number "10")

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:

Select branch(es) of interest
Right-click to get acces to the Branch Context Menu
Choose "Edit Edge Label" to provide a text-label for the branch - any gaps in your text will be substituted by "_" characters on the label

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:

File->Save
File->Save As...

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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