Help - Branch
A branch is an object in a TreeGraph-document which connects two nodes with each other and therefore has a major role in defining the tree topology. Branches can also carry labels and hidden branch data. The branch leading to the root node of the document is the only branch connected to only one node. You can use the document formats to specify whether the root branch shall be displayed or not.
Contents
Branch length
For every branch a floating point value representing the length of this branch can be stored. Branch lengths can be displayed as stored if an according view mode is selected and could e.g. be used illustrate the time that passed during the evolution of the two taxa connected by that branch.
The equivalence of branch length units to the displayed length can be specified by the "Distance per branch length"-property in the "Branches and labels"-tab of the document formats-dialog.
It is important not to confuse the branch length with the minimal branch length format which is used to manually edit distances between different tree elements (see below).
Branch formats
A branch is a line element and therefore all line formats can be applied. Additionally there are the following specific formats. You can change the branch and line formats using the element formats-dialog.
Minimal branch length
The minimal branch length is used to make sure that a branch is never shorter than a given value even if the positions of other elements (like labels) would allow this. In contrast to the exact branch length (see above), which could e.g. represent a time-value, the minimal branch length is a format. It should be used for layout purposes only, e.g. if an image or any other type of label not supported by TreeGraph should be manually placed near the branch after exporting the document to an image file.
Minimal space above
The space that should be left between the branch and the next element above even if the positions of the other elements in the tree would allow to leave less space. The advantage of this format is the same as for the minimal branch length.
Minimal space below
The space that should be left between the branch and the next element below even if the positions of the other elements in the tree would allow to leave less space. The advantage of this format is the same as for the minimal branch length.
Constant width
If the option constant width is checked, the branch is displayed as a line with a constant width. (The line width is part of the line formats.) Otherwise the branch has the line width of its parent node at the beginning (left side) and its own line width at the end (right side).
Constant line widths could e.g. be used to illustrate substitution rates along branches, whereas narrowing lines could be used to mark a terminal node representing a whole group of taxa.
Branch line width is used to mark a larger taxon group, e.g. a collpased clade not shown in detail.
A constant branch line width can be used e.g. to illustrate rates or other node/branch data (see Set distance values by node/branch data).
