How do I install the Esl Shuffle skill?

Run npx skillmds add vimalinx/esl-shuffle 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 Shuffle safe to use?

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Which AI agents work with Esl Shuffle?

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 Shuffle free to use?

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

Who published Esl Shuffle?

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

Esl Shuffle by vimalinx — Agent Skill

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

File contents

esl-shuffle

Quick Start

Command: esl-shuffle [options] <seqfile> (shuffle sequences)
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-shuffle
Help: See references/help.md for full options (access with -h)

When To Use This Tool

Use esl-shuffle when you need randomized controls derived from existing sequences or alignments.
Default mode shuffles individual sequences; -A switches to multiple-alignment shuffling; -G generates de novo random sequences.
Reach for -d, -0, -1, -w, or -r when you want a specific preservation model for sequence-based controls.
Use -b or -v in -A mode for bootstrap-like or per-column randomized alignment controls.

Common Patterns

# Shuffle each input sequence while preserving monoresidue composition
esl-shuffle sequences.fa > shuffled.fa

# Preserve diresidue composition exactly
esl-shuffle -d sequences.fa > diresidue.fa

# Bootstrap alignment columns with replacement
esl-shuffle -A -b alignment.sto > bootstrap.sto

# Generate 10 random RNA sequences of length 80
esl-shuffle -G --rna -N 10 -L 80 > random-rna.fa

# Reproducible amino-acid generation
esl-shuffle -G --amino --seed 17 -N 3 -L 50 > random-aa.fa

Recommended Workflow

Pick the correct mode first: default sequence shuffling, -A for alignments, or -G for de novo generation.
Choose the randomization scheme that matches the null model you actually need.
Add -N, -L, and --seed if you need multiple samples, fixed lengths, or reproducibility.
Force --informat <fmt> when autodetection is ambiguous.
Validate a few outputs to ensure the preserved statistics match your intended control design.

Guardrails

-h works; --help and --version are rejected by the local executable.
Local -h advertises --rna as the default alphabet in -G mode, but the installed man page says one of --rna, --dna, or --amino must be selected. Pass the alphabet explicitly to avoid ambiguity.
Default mode and -A need an input file; -G does not.
-b and -v only make sense in -A mode, while -d, -0, -1, -r, and -w are sequence-mode operations.
-L truncates outputs as well as setting generated-sequence length, so do not enable it casually on aligned data.

---name: esl-shuffledescription: Use when shuffling biological sequences, bootstrapping alignment columns, or generating de novo random RNA, DNA, or protein controls.--- # esl-shuffle ## Quick Start - **Command:** `esl-shuffle [options] <seqfile>` (shuffle sequences) - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/esl-shuffle` - **Help:** See `references/help.md` for full options (access with `-h`) ## When To Use This Tool - Use `esl-shuffle` when you need randomized controls derived from existing sequences or alignments. - Default mode shuffles individual sequences; `-A` switches to multiple-alignment shuffling; `-G` generates de novo random sequences. - Reach for `-d`, `-0`, `-1`, `-w`, or `-r` when you want a specific preservation model for sequence-based controls. - Use `-b` or `-v` in `-A` mode for bootstrap-like or per-column randomized alignment controls. ## Common Patterns ```bash # Shuffle each input sequence while preserving monoresidue composition esl-shuffle sequences.fa > shuffled.fa # Preserve diresidue composition exactly esl-shuffle -d sequences.fa > diresidue.fa # Bootstrap alignment columns with replacement esl-shuffle -A -b alignment.sto > bootstrap.sto # Generate 10 random RNA sequences of length 80 esl-shuffle -G --rna -N 10 -L 80 > random-rna.fa # Reproducible amino-acid generation esl-shuffle -G --amino --seed 17 -N 3 -L 50 > random-aa.fa ``` ## Recommended Workflow 1. Pick the correct mode first: default sequence shuffling, `-A` for alignments, or `-G` for de novo generation. 2. Choose the randomization scheme that matches the null model you actually need. 3. Add `-N`, `-L`, and `--seed` if you need multiple samples, fixed lengths, or reproducibility. 4. Force `--informat <fmt>` when autodetection is ambiguous. 5. Validate a few outputs to ensure the preserved statistics match your intended control design. ## Guardrails - `-h` works; `--help` and `--version` are rejected by the local executable. - Local `-h` advertises `--rna` as the default alphabet in `-G` mode, but the installed man page says one of `--rna`, `--dna`, or `--amino` must be selected. Pass the alphabet explicitly to avoid ambiguity. - Default mode and `-A` need an input file; `-G` does not. - `-b` and `-v` only make sense in `-A` mode, while `-d`, `-0`, `-1`, `-r`, and `-w` are sequence-mode operations. - `-L` truncates outputs as well as setting generated-sequence length, so do not enable it casually on aligned data.

Frequently asked questions