hmmemit

name	hmmemit
description	Use when sampling synthetic sequences, alignments, or consensus sequences from one or more profile HMMs.
disable-model-invocation	true
user-invocable	true

hmmemit

Quick Start

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

When To Use This Tool

• Use hmmemit when you need synthetic positives or consensus representatives derived from profile HMMs.
• Default mode samples unaligned sequences from the core probability model; -a emits alignments, -c emits simple consensus sequences, -C emits thresholded fancy consensus sequences, and -p samples from the fully configured search profile.
• It is useful for benchmark generation, smoke tests, demo data, or sanity-checking what a model prefers.

Common Patterns

# Sample one sequence per model from the core model
hmmemit profiles.hmm > samples.fa

# Emit 20 aligned synthetic sequences per model
hmmemit -a -N 20 profile.hmm > emitted.sto

# Emit plurality-rule consensus sequences
hmmemit -c profile.hmm > consensus.fa

# Sample homolog-like sequences from the fully configured search profile
hmmemit -p -L 800 --glocal -N 10 profile.hmm > profile-samples.fa

Recommended Workflow

1. Decide whether you want sampled sequences, alignments, or consensus output.
2. Set -N and --seed before generating benchmark data so the run is reproducible and large enough for the test you care about.
3. Use -p only when you explicitly want search-profile behavior such as local or glocal configuration and length modeling.
4. Redirect the emitted output immediately into a named FASTA or Stockholm file.
5. If you generated multiple models' output from a library, keep the original HMM names so downstream provenance remains clear.

Guardrails

• -h works; --help and --version are rejected by the local executable.
• Despite the short usage string saying <hmmfile (single)>, runtime testing shows the tool will iterate across a multi-model HMM library and emit output for each model.
• -L, --local, --unilocal, --glocal, and --uniglocal only apply with -p.
• --minl and --minu only make sense with -C.
• hmmfile may be - to read a profile stream from stdin.