hmmlogo

name	hmmlogo
description	Use when extracting per-position residue-height and indel-rate data from a profile HMM for sequence-logo visualization.
disable-model-invocation	true
user-invocable	true

hmmlogo

Quick Start

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

When To Use This Tool

• Use hmmlogo when you need the underlying numeric data for a profile logo rather than a rendered image.
• It computes per-position residue heights plus indel-related values that can be passed into custom plotting code or compared across models.
• Reach for different --height_* modes depending on whether you want relative-entropy style stacks or score-driven letter heights.

Common Patterns

# Dump default relative-entropy logo data plus indel table
hmmlogo profile.hmm > logo.txt

# Show only letters above background probability
hmmlogo --height_relent_abovebg profile.hmm > logo-abovebg.txt

# Use score-based heights and omit the indel table
hmmlogo --height_score --no_indel profile.hmm > score-logo.txt

Recommended Workflow

1. Start from a validated HMM profile file rather than raw sequences or an alignment.
2. Run the default mode once to understand the output structure for your model.
3. Pick the height scheme that matches the biological or visualization question.
4. Feed the resulting tables into a plotting step of your choice; hmmlogo itself does not draw the final figure.
5. Keep the HMM and logo-data files together so later figure regeneration stays traceable.

Guardrails

• Input must be a valid HMM profile file, not raw sequences or alignments.
• Runtime testing shows the default output is plain text tables beginning with lines such as max expected height = ... and Residue heights; it is not an image or SVG.
• -h works, but the autogenerated references/help.md capture for --help / --version is misleadingly minimal. Use -h for real help.
• --no_indel suppresses the indel-rate table only; it does not change residue-height calculations.
• The meaning of total stack height changes across --height_relent_all, --height_relent_abovebg, and --height_score, so do not compare plots across modes without labeling them clearly.