v3.1.0
New features
- The CLI program
gctree infer
writes a pickledCollapsedTree
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
andCollapsedForest
are exposed at package level, so they can be imported directly rather than from thebranching_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.