Hmmstat

hmmstat

Quick Start

• Command: hmmstat <hmmfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmstat
• Version: HMMER 3.4
• Full reference: See references/help.md

When To Use This Tool

• Sanity-check an HMM file after hmmbuild or before hmmpress.
• Inspect model counts and basic summary statistics in a profile collection.
• Confirm that a file is parseable as a valid HMMER profile library before heavier downstream jobs.

Common Patterns

# 1) Print summary statistics for one HMM collection
hmmstat profiles.hmm

# 2) Inspect a large library and page through the summary
hmmstat Pfam-A.hmm | less -S

Recommended Workflow

1. Run hmmstat immediately after generating or downloading a profile collection.
2. Check that the number of models, alphabet expectations, and general summary layout look plausible.
3. If the file is structurally sound, move on to hmmpress, hmmsearch, hmmscan, or hmmfetch.
4. If the summary is surprising, inspect the source HMM file before investing compute in longer searches.

Guardrails

• This is a read-only reporting tool; it does not repair or modify HMM files.
• It expects exactly one positional HMM file argument.
• Use -h for help; --help and --version are not accepted here.
• Treat its text output as a summary for humans first; if you need machine-stable metadata, keep the original HMM file around too.