Additional required tools:

16S ASV analysis:

• aligned_nearest_neighbor (https://github.com/yk23/aligned_nearest_neighbor) -- tool for quickly computing nearest-neighbor queries from a test taxa set onto a training taxa set. Necessary to implement baseline methods.

Installation

Install the gem package and all dependencies:

pip install -e ".[notebooks,evo]"

• Base install (-e .): core gem package, ML/bioinformatics dependencies
• notebooks: adds geopandas and pycountry for visualization notebooks
• evo: adds evo-model and flash-attn (requires a CUDA-enabled build environment)

For Evo2 support (not on PyPI, install from source separately):

pip install git+https://github.com/ArcInstitute/evo2.git