We should document the options. What I suggest we do is clearly describe the problem and how it is solved with the various methods we are implementing. Therefore, we should do the following:
Describe the problem PTP attempts to solve (fitting branch lengths into two exponential distributions), and the motivation behind it.
Describe the two options, single- and multi-rate solutions.
If we are to implement GMYC then we should explain the problem/motivation as well.
Document the options of our implementation.
Have a clear example (a figure of a tree) with a demo execution of the program, and explain the output.
Document the outgroup option part (how the LCA is computed, and why only two tips are required to select the LCA).
xflouris
commented
9 years ago
We should document the options. What I suggest we do is clearly describe the problem and how it is solved with the various methods we are implementing. Therefore, we should do the following: