Closed mattjones315 closed 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?
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.
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.