The AAanalysis Ecosystem
AAanalysis is the interpretable middle layer between bioinformatics I/O and the
downstream machine-learning, explainable-AI, causal, and protein-design stack. The
map below shows the Python packages it complements upstream (sequences, embeddings,
structures, omics) and downstream (models, optimization, design, XAI evaluation),
and where its own classes (Part × Split × Scale · AAontology · CPP · TreeModel ·
ShapModel · …) fit in between.