added tree.py and reconstruct.py to match this framework
added functional example notebook that builds full MD2 dataset from start to finish
all extra files (especially from phyml and paml) spit out into project directory
Possible issues/things to think about:
haven't worked out reading in previous data (for example, an old alignment) and running pipeline from there. Current hack is to use pandas.read_csv function. Need to incorporate as a phylogenetics tool? With appropriate checks to ensure it's a phylopandas df
project.current?
no metadata.json file yet - currently writing out each step as a csv in the project_dir, and then have history.json file
haven't yet incorporated df_editor, or checks for manual df operations by user
future things: tutorial, easy install instructions for users (Windows...), tree visualization, etc
Possible issues/things to think about: