Slatkin Maddison

[spond]

Dear @stephenshank,

We should also implement a web app and a standalone command line tool for performing the Slatkin Maddison test for compartmentalization with visual feedback, such as labeling the branches where transitions occur, and coloring branches based on the results of the permutation test.

All the components are already there, like the parsimony state reconstruction, so the test should be easy to implement.

The standalone (node) version should request branch partitioning regular expression from the command line. You can run through the S-M implementation in HyPhy to get a sense of what the result should be.

Best, Sergei