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