TreeView Help: Scale bar

If the tree being viewed has branch lengths, and you are viewing the tree as either unrooted or as a phylogram, then TreeView displays a scale bar in the bottom left corner of the tree window:

scale bar

The units for this scale depend on those used to construct the tree. For example, most tree-building programs output distances as numbers of substitutions per site. For such trees TreeView typically displays a scale of "0.1", meaning 0.1 nucleotide substitutions per site. The actual value will depend on the branch lengths in the tree.

Other trees, such as those computed using parsimony, may have integer branch lengths (i.e., 1, 5, 10), and hence the scale bar will be in units appropriate to the tree. For example, a value of "10" means 10 steps.

One note of caution concerns "branch lengths" on trees obtained using PHYLIP's CONSENSE program. These branch lengths are actually the frequency of the corresponding clade in the set of input trees (if the trees were bootstrap trees then these correspond to bootstrap values). Because PHYLIP puts these numbers where TreeView expects the branch lengths, TreeView will display a scale bar. Ignore this! It is best to display PHYLIP consensus trees as rectangular cladograms.