How do I install the Esl Weight skill?

Run npx skillmds add vimalinx/esl-weight in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Esl Weight safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Esl Weight?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Esl Weight free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Esl Weight?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Esl Weight by vimalinx — Agent Skill

Name: Esl Weight
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

esl-weight

Quick Start

Command: esl-weight [options] <msafile>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-weight
Full reference: See references/help.md for the current startup failure; option details below are grounded in the local man page plus binary strings.

When To Use This Tool

Use esl-weight when you need per-sequence weights written back into a multiple alignment as Stockholm #=GS <seqname> WT <weight> annotation.
It is useful before downstream profile-model building or when you want an explicit, inspectable weighted alignment artifact.
Reach for -g for Gerstein/Sonnhammer/Chothia weights, -p for Henikoff position-based weights, or -b for BLOSUM-style cluster weights.

Common Patterns

# Default Gerstein/Sonnhammer/Chothia weighting
esl-weight alignment.sto > weighted.sto

# Faster Henikoff position-based weighting
esl-weight -p alignment.sto > pb-weighted.sto

# BLOSUM-style clustering weights at a chosen identity threshold
esl-weight -b --id 0.70 alignment.sto > blosum70.sto

# Force protein alphabet when autodetection is ambiguous
esl-weight --amino alignment.sto > weighted-aa.sto

Recommended Workflow

Fix the local shared-library issue first so the binary can start.
Prepare the input multiple alignment and force the alphabet with --amino, --dna, or --rna if autodetection could be ambiguous.
Choose the weighting rule that matches the downstream method.
Inspect the emitted Stockholm alignment and confirm #=GS ... WT lines are present.
Feed the weighted alignment into the next modeling step only after the annotations look plausible.

Guardrails

The local executable currently fails to start because libopenblas.so.0 is missing. Until that library issue is fixed, -h and live runtime validation are unavailable.
Despite the startup failure, the local man page documents -g as the default, -p as Henikoff position-based weighting, and -b as BLOSUM-style clustering weights.
--id <x> only applies with -b; the documented default threshold is 0.62.
Output is written in Stockholm format with WT annotations even if the input alignment came from another accepted format.
Option details here are intentionally conservative because the current environment cannot execute the binary end-to-end.

---name: esl-weightdescription: Use when adding Stockholm sequence-weight annotations to nucleotide or protein MSAs before downstream HMMER-style modeling.--- # esl-weight ## Quick Start - **Command:** `esl-weight [options] <msafile>` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/esl-weight` - **Full reference:** See `references/help.md` for the current startup failure; option details below are grounded in the local man page plus binary strings. ## When To Use This Tool - Use `esl-weight` when you need per-sequence weights written back into a multiple alignment as Stockholm `#=GS <seqname> WT <weight>` annotation. - It is useful before downstream profile-model building or when you want an explicit, inspectable weighted alignment artifact. - Reach for `-g` for Gerstein/Sonnhammer/Chothia weights, `-p` for Henikoff position-based weights, or `-b` for BLOSUM-style cluster weights. ## Common Patterns ```bash # Default Gerstein/Sonnhammer/Chothia weighting esl-weight alignment.sto > weighted.sto # Faster Henikoff position-based weighting esl-weight -p alignment.sto > pb-weighted.sto # BLOSUM-style clustering weights at a chosen identity threshold esl-weight -b --id 0.70 alignment.sto > blosum70.sto # Force protein alphabet when autodetection is ambiguous esl-weight --amino alignment.sto > weighted-aa.sto ``` ## Recommended Workflow 1. Fix the local shared-library issue first so the binary can start. 2. Prepare the input multiple alignment and force the alphabet with `--amino`, `--dna`, or `--rna` if autodetection could be ambiguous. 3. Choose the weighting rule that matches the downstream method. 4. Inspect the emitted Stockholm alignment and confirm `#=GS ... WT` lines are present. 5. Feed the weighted alignment into the next modeling step only after the annotations look plausible. ## Guardrails - The local executable currently fails to start because `libopenblas.so.0` is missing. Until that library issue is fixed, `-h` and live runtime validation are unavailable. - Despite the startup failure, the local man page documents `-g` as the default, `-p` as Henikoff position-based weighting, and `-b` as BLOSUM-style clustering weights. - `--id <x>` only applies with `-b`; the documented default threshold is `0.62`. - Output is written in Stockholm format with `WT` annotations even if the input alignment came from another accepted format. - Option details here are intentionally conservative because the current environment cannot execute the binary end-to-end.

Frequently asked questions