hmmsim

Quick Start

• Command: hmmsim [options] <hmmfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmsim
• Full reference: See references/help.md

When To Use This Tool

• Measure how a profile HMM scores random sequences.
• Explore score and E-value behavior under different random-sequence lengths and sample counts.
• Benchmark HMM filtering or calibration behavior before deploying a profile in larger search pipelines.
• Generate score-distribution outputs for debugging or method development around HMMER models.

Common Patterns

# 1) Collect a basic score distribution for one profile HMM
hmmsim \
  mymodel.hmm

# 2) Increase the number and length of random targets
hmmsim \
  -N 10000 \
  -L 300 \
  mymodel.hmm

# 3) Write verbose scores and an E-value calibration plot payload
hmmsim \
  -v \
  --efile hmmsim.eplot.tsv \
  -o hmmsim.out \
  mymodel.hmm

Recommended Workflow

1. Prepare a valid profile HMM file and decide whether you need a quick default run or a larger calibration experiment with explicit -N and -L.
2. Choose the scoring/alignment mode (--vit, --fwd, --hyb, --msv, --fs, --sw, --ls, --s) if you are studying a specific HMMER behavior.
3. Run hmmsim and direct outputs to files with -o, --efile, --ffile, or related options when you want reusable diagnostic artifacts.
4. Interpret the result as a random-sequence score-distribution study, not as a biologically realistic sequence-generation workflow.

Guardrails

• hmmsim evaluates an HMM against random sequences; it is not a general simulator for generating biologically realistic sequences from a model.
• Use -h for help; --help and --version are not supported.
• The input must be a valid HMMER profile HMM file.
• Defaults are relatively small (-N 1000, -L 100), so set them explicitly for serious calibration or benchmarking work.