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YosefLab / Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
https://cassiopeia-lineage.readthedocs.io/en/latest/
MIT License
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Small Parsimony #117

Closed mattjones315 closed 3 years ago

mattjones315 commented 3 years ago

Implements the first section of small parsimony tools, supporting the Fitch-Hartigan algorithm and small parsimony computations.

Also adds the tools module which will store all post-tree-reconstruction tools (e.g., small parsimony, evolutionary coupling, etc.).

While this PR only implements the Fitch-Hartigan small-parsimony algorithm, we will continue to populate this library with several post-reconstruction tools.

Lioscro commented 3 years ago

@mattjones315 Oh, also, I notice in the description you mention evolutionary coupling, but I don't remember seeing anything about that in the changes. Are you still trying to get those in this PR?

mattjones315 commented 3 years ago

Thanks for the review Joseph! I believe I've hit all of your comments.

To note, this PR is only the first of several additions to the tools directory. Currently, I'm only implementing Fitch-Hartigan because I don't want to do too much in one PR. I'll move onto FitchCount and other tools in subsequent PRs.