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Assign Branch Lengths

The branch lengths of the trees can be modified if desired. To modify the branch lengths select Trees->Assign Branch Lengths... and the options window will open. In addition, if branch lengths are absent in the trees in the file a window will automatically be displayed allowing the user to define the lengths.


The following options are available:

  1. Fixed lengths: A fixed length, v, is assigned to each branch.
  2. Fixed tree height: A fixed height, T, is assigned to each tree in which it defines the distance from each tip node to the root. The resulting tree is ultrametric.
  3. Random uniform: Branch length values are assigned by being radomly drawn from a uniform distribution on an interval, U[x,y], determined by the user (the interval must be positive). The user can select to sort the values and assign the values by forcing small or large values to the tips.
  4. Random exponential: branch length values are assigned by being radomly drawn from an exponential distribution defined by the parameter, λ, determined by the user (the parameter must be positive). The user can select to sort the values and assign the values by forcing small or large values to the tips.
  5. Birth-death: Branch length values are assigned by sampling from the birth-death method described by Rannala and Yang (1996). The birth-death distribution is described by four parameters: the speciation rate, λ, the extinction rate, μ, the taxon sampling rate, ρ, and the tree depth or height, T. The speciation rate, taxon sampling rate, and the tree depth must be >0.