How do I install the Esl Alimanip skill?

Run npx skillmds add vimalinx/esl-alimanip 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.

What does the Esl Alimanip skill do?

Use when manipulating multiple sequence alignment files using Easel tools from HMMER. It is listed under Coding & Dev Tools on SkillMD.

Is Esl Alimanip 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 Alimanip?

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 Alimanip free to use?

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

Who published Esl Alimanip?

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

Esl Alimanip by vimalinx — Agent Skill

Name: Esl Alimanip
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

esl-alimanip

Quick Start

Command: esl-alimanip
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alimanip
Reference: See references/help.md for full options and usage

When To Use This Tool

Use esl-alimanip when you need structural edits to an alignment that go beyond simple reformatting or column masking.
It is intended for sequence removal/retention, reordering, trimming to subsequences, RF-related manipulations, annotation numbering, and other Stockholm/Pfam-centric alignment surgery.
Use it when curating a multiple sequence alignment before HMM building or comparative analysis.
In this environment it is currently blocked by a missing libopenblas.so.0, so treat the syntax below as documented behavior that cannot be executed until the library issue is fixed.

Common Patterns

# Keep only sequences listed in a file
esl-alimanip --seq-k keep.txt alignment.sto > kept.sto

# Remove sequences listed in a file
esl-alimanip --seq-r remove.txt alignment.sto > filtered.sto

# Trim alignment sequences to subsequences from a companion file
esl-alimanip --trim subseqs.fa alignment.sto > trimmed.sto

# Add numbering over nongap RF columns
esl-alimanip --num-rf alignment.sto > numbered.sto

Recommended Workflow

Verify the shared-library problem is resolved before relying on this tool in the current environment.
Choose one alignment-editing goal at a time: sequence keep/remove, trimming, reordering, RF/mask manipulation, or annotation conversion.
Apply the relevant option set to the source Stockholm/Pfam alignment and write to a new file rather than in place.
Validate the edited alignment with downstream Easel tools before further analysis.

Guardrails

Ensure shared library dependencies (libopenblas) are available in the environment
Consult references/help.md for supported alignment formats and options
Verify alignment integrity after any manipulation operation
Many higher-level options depend on Stockholm/Pfam markup such as #=GC RF, #=GR POST, or per-sequence GS tags; absent annotation will make those modes fail

---name: esl-alimanipdescription: Use when manipulating multiple sequence alignment files using Easel tools from HMMER.--- # esl-alimanip ## Quick Start - **Command:** `esl-alimanip` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/esl-alimanip` - **Reference:** See `references/help.md` for full options and usage ## When To Use This Tool - Use `esl-alimanip` when you need structural edits to an alignment that go beyond simple reformatting or column masking. - It is intended for sequence removal/retention, reordering, trimming to subsequences, RF-related manipulations, annotation numbering, and other Stockholm/Pfam-centric alignment surgery. - Use it when curating a multiple sequence alignment before HMM building or comparative analysis. - In this environment it is currently blocked by a missing `libopenblas.so.0`, so treat the syntax below as documented behavior that cannot be executed until the library issue is fixed. ## Common Patterns ```bash # Keep only sequences listed in a file esl-alimanip --seq-k keep.txt alignment.sto > kept.sto # Remove sequences listed in a file esl-alimanip --seq-r remove.txt alignment.sto > filtered.sto # Trim alignment sequences to subsequences from a companion file esl-alimanip --trim subseqs.fa alignment.sto > trimmed.sto # Add numbering over nongap RF columns esl-alimanip --num-rf alignment.sto > numbered.sto ``` ## Recommended Workflow 1. Verify the shared-library problem is resolved before relying on this tool in the current environment. 2. Choose one alignment-editing goal at a time: sequence keep/remove, trimming, reordering, RF/mask manipulation, or annotation conversion. 3. Apply the relevant option set to the source Stockholm/Pfam alignment and write to a new file rather than in place. 4. Validate the edited alignment with downstream Easel tools before further analysis. ## Guardrails - Ensure shared library dependencies (libopenblas) are available in the environment - Consult `references/help.md` for supported alignment formats and options - Verify alignment integrity after any manipulation operation - Many higher-level options depend on Stockholm/Pfam markup such as `#=GC RF`, `#=GR POST`, or per-sequence GS tags; absent annotation will make those modes fail

Frequently asked questions