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Create a wiki page with documentation #12

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xflouris opened this issue Jul 13, 2015 · 1 comment
Open

Create a wiki page with documentation #12

xflouris opened this issue Jul 13, 2015 · 1 comment
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@xflouris
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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
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started working on this

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