Help - View modes

From TreeGraph help
Jump to: navigation, search

The current version of TreeGraph offers two view modes to display your tree. You can change the view mode either by selecting it from the view menu or the tool bar. The currently selected view mode is also used when a tree is exported as a graphic or PDF.

Rectangular cladogram

Example of a rectangular cladogram

This view mode does not display any of the branch length that might be stored in the branches of the document. Instead the displayed branch lengths are determined only by the following formats:

  • Each branch has at least the length that is defined by its minimal branch length format.
  • Furthermore it is displayed longer if the attached labels need more space.
  • Beyond that the branch lengths are organized in a way that all terminal nodes are located below each other (start at the same x-coordinate). That means that some branches may be elongated to achieve this.

This view mode also allows you to display internal nodes with the specified corner radius.

Phylogram/ Chronogram

Example of a chronogram with a scale bar

A phylogram is phylogenetic tree where the branch lengths are proportional to the number of evolutionary events that took place along this branch (e.g. number of substituions) whereas a chronogram displays the time that passed along a branch. If you want to display any of these parameters with TreeGraph 2 you have to store the according data as the branch length (see Importing Nexus and Newick files or Copying node/branch data for details). You can adjust how much millimeters a branch lengths unit should make up in the document formats.

When you select the phylogram/ chronogram-view mode the branch lengths are only determined by the value stored in the branch length field whereas formats that are followed in the rectangular cladogram-view mode (minimal branch length, corner radius the space that the attached label blocks need) are ignored. Furthermore choosing this view mode only makes sense if all branch lengths of the document are specified. If a branch has an undefined length it will be displayed with a default length which does not change if the distance per branch length unit is changed.

In the phylogram/ chronogram-view mode it can be helpful to use a scale bar to point out the meaning of the branch lengths. Note that TreeGraph 2 offers many additional ways to display node/branch data e.g. with labels or by the line width or line color. (See Set distance values by node/branch data or Set colors by node/branch data for details.)

See also