v3.1.0

New features

• The CLI program gctree infer writes a pickled CollapsedTree object for each parsimony tree, which can be later loaded and manipulated via the API.
• Updates to CollapsedTree.render to annotate amino acid substitutions, and associated new parameters in API and CLI. Note: these parameters are not supported by the scons pipelines, which are deprecated.
• Classes CollapsedTree and CollapsedForest are exposed at package level, so they can be imported directly rather than from the branching_processes module.
• Many improvements in documentation: matsengrp.github.io/gctree

Developer notes

• The branching_processes module has been refactored to remove illegitimate inheritance
• Better default p, q parameters for MLE avoid gradient warnings.