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GeMMA, the step of the FunFam protocol that builds a superfamily's tree from S90 clusters of its Gene3D sequences

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UCL/cath-gemma

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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).

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GeMMA, the step of the FunFam protocol that builds a superfamily's tree from S90 clusters of its Gene3D sequences

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