Byte-reproducible
Same inputs, same outputs, across --cpus, --batch_size, --prefetch_targets and
PYTHONHASHSEED, for the dependency set in uv.lock.
mgnifam
Iterative HMM-based protein family generation over very large sequence databases.
Given a chunk of MMseqs2 clusters and a protein FASTA, mgnifam generate_families builds an
HMM from each cluster, recruits new members from the whole database, re-aligns, and
either converges on a family or discards the cluster. It is the core algorithm of the
mgnifams Nextflow pipeline, extracted into
a standalone, tested package.
Built for billions
Targets stream from disk, random access goes through an Easel SSI index, and families
are searched in batched hmmsearch waves.
Installationpip, uv, bioconda, or a locked checkout.
Generating familiesFrom clusters to converged HMM families.
Updating familiesRefresh existing models against a new release.
OutputsEvery file written, exit status, and the MultiQC summary.