CATH-eMMA

Overview

Fork of CATH-Gemma switching the core from HHsuite to embeddings or structural distances. Main features/wishlist

• Revised protocol to use MMseqs2 instead of CD-HIT.
• Wrap pipeline in Python
• Add flags to use either embedding distances or 1/bitscore distances from Foldseek.
• Create infrastructure for multiple iterations (MARC)
• Create partitions using MDAs

This repo is part of the FunFams pipeline as an intermediate step before FunFHMMER. The master FunFams repo is https://github.com/UCL/cath-funfam

See the GeMMA Wiki for documentation (to expand with new usage).