New features
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- The CLI program [`gctree infer`](https://matsengrp.github.io/gctree/cli.html#infer) writes a pickled [`CollapsedTree`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html) object for each parsimony tree, which can be later loaded and manipulated via the API.
- Updates to [`CollapsedTree.render`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html#gctree.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`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html) and [`CollapsedForest`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedForest.html) are exposed at package level, so they can be imported directly rather than from the [`branching_processes`](https://github.com/matsengrp/gctree/blob/master/gctree/branching_processes.py) module.
- Many improvements in documentation: [matsengrp.github.io/gctree](https://matsengrp.github.io/gctree/)
Developer notes
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- The [`branching_processes`](https://github.com/matsengrp/gctree/blob/master/gctree/branching_processes.py) module has been refactored to remove illegitimate inheritance
- Better default `p, q` parameters for MLE avoid gradient warnings.