Hmmpress

hmmpress

Quick Start

• Command: hmmpress [-options] <hmmfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmpress
• Version: HMMER 3.4
• Full reference: references/help.md

When To Use This Tool

• Prepare a text HMM database for repeated hmmscan use.
• Create the binary sidecar files that accelerate HMM database access.
• Re-press a database after rebuilding or concatenating HMMs.
• This is a database-preparation step, not a search step.

Common Patterns

# 1) Press an HMM database once
hmmpress Pfam-A.hmm

# 2) Force regeneration of pressed sidecar files
hmmpress -f custom_models.hmm

Recommended Workflow

1. Build or collect all text-format HMMs into one database file.
2. Run hmmpress once on that file.
3. Confirm the .h3m, .h3i, .h3f, and .h3p sidecars appear beside the source .hmm.
4. Use the pressed database with hmmscan for repeated annotation jobs.

Guardrails

• hmmpress prepares sidecar indexes for faster HMM database access and is primarily relevant to hmmscan workflows.
• The original .hmm file must remain in place; hmmpress does not replace it.
• Use -f if you intentionally want to overwrite previous pressed files.
• Use -h for help; --help and --version are not valid here.