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Pyvolve v0.8.2

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@sjspielman sjspielman released this 18 May 16:45
· 49 commits to master since this release

Two primary updates:

  1. Custom models can now be provided with custom state frequencies. To provide custom state frequencies, the provided matrix must be symmetric. Under any circumstance, the rows of the matrix should sum to 0 (whether frequencies are provided or not!)
  2. Codon models (GY, MG) can now be scaled such that branch lengths indicate the mean number of neutral substitutions per unit time. To invoke, include the argument: neutral_scaling=True when defining a Model object, for example:
    m = Model("GY", {"omega":0.4}, neutral_scaling=True.