hmmconvert

name	hmmconvert
description	Use when converting profile HMM files between HMMER3 ASCII or binary, legacy HMMER2, or specific 3.x text revisions.
disable-model-invocation	true
user-invocable	true

hmmconvert

Quick Start

• Command: hmmconvert [-options] <hmmfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmconvert
• Full reference: See references/help.md for --help failure behavior and hmmconvert -h output

When To Use This Tool

• Use hmmconvert when downstream tools or archival constraints require a different HMMER profile-file format than the one you currently have.
• It is useful for converting between current HMMER3 ASCII, HMMER3 binary, legacy HMMER2 ASCII, or older named HMMER3 text revisions such as 3/a through 3/f.
• Reach for it when comparing historical model files, shrinking storage with binary output, or preparing data for older compatibility experiments.

Common Patterns

# Rewrite a profile file in the current HMMER3 ASCII format
hmmconvert profiles.hmm > profiles.3f.hmm

# Convert to HMMER3 binary format
hmmconvert -b profiles.hmm > profiles.h3m

# Convert to legacy HMMER2-style ASCII for comparison work
hmmconvert -2 profiles.hmm > profiles.hmmer2

# Read from stdin and pin an older HMMER3 text revision explicitly
cat profiles.hmm | hmmconvert --outfmt 3/b - > profiles.3b.hmm

Recommended Workflow

1. Decide what exact target format the next consumer needs before converting anything.
2. Preserve the original profile file so you can diff or fall back after conversion.
3. Run hmmconvert and redirect stdout to an explicitly named output file.
4. Validate the converted file with hmmstat, hmmfetch, or the downstream HMMER tool you actually care about.

Guardrails

• -h works; --help and --version are rejected by the local executable.
• Output goes to stdout, so forgetting redirection will dump the converted profile into the terminal session.
• Input hmmfile may be - to read from stdin.
• -2 produces an approximate backward-compatible HMMER2 ASCII form, not a perfect round-trip of every HMMER3 feature.
• --outfmt applies only to named HMMER3 ASCII revisions, not binary or HMMER2 output.