How do I install the Systematic Mutations skill?

Run npx skillmds add vimalinx/systematic-mutations 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 Systematic Mutations safe to use?

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

Which AI agents work with Systematic Mutations?

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 Systematic Mutations free to use?

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

Who published Systematic Mutations?

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

Systematic Mutations by vimalinx — Agent Skill

Name: Systematic Mutations
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

systematic-mutations

Tiny bash filter over transmute -replace. It reads sequence [pattern] records from stdin, uppercases the sequence, substitutes A, C, G, and T at every position, optionally appends the second whitespace-delimited field after a colon, then case-insensitively sorts and deduplicates the emitted variants.

Quick Start

Command: echo ATGAAACCCGGGTTTTAG | systematic-mutations
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/systematic-mutations
Required dependency: transmute on PATH

When To Use This Tool

Generating every single-base substitution of a short sequence
Expanding disambiguated sequence sets into explicit A/C/G/T mutation catalogs
Keeping an attached pattern/label while mutating the leading sequence token
Building small exhaustive mutation sets in a shell pipeline without writing custom code

Common Patterns

# Enumerate all single-position substitutions
echo ATGAAACCCGGGTTTTAG | systematic-mutations

# Preserve a second-column pattern label
echo 'ATG tag1' | systematic-mutations

# Expand ambiguous input first, then enumerate mutations
echo RCCGGY | disambiguate-nucleotides | systematic-mutations

Recommended Workflow

Feed one sequence per line on stdin, optionally followed by one extra whitespace-delimited label/pattern.
Normalize ambiguous bases upstream if you need explicit A/C/G/T inputs before mutation expansion.
Pipe the output directly into downstream text filters, because this tool does not create files by itself.
Deduplicate or rank the resulting variant strings downstream only if you need more than the built-in case-insensitive uniqueness pass.

Guardrails

This script ignores command-line flags. Local testing showed systematic-mutations -h is silent with no stdin and behaves exactly like the normal mutator when stdin is present.
Input is read from stdin only; the first whitespace-delimited token is the sequence and the second token, if present, is preserved as :<pattern>. Additional columns are ignored.
The original sequence can reappear in the output because the substitution loop also tries the existing base at each position before the final sort -f | uniq -i.
The script depends on transmute -replace; if transmute is missing from PATH, mutation generation fails.

---name: systematic-mutationsdescription: Use when enumerating all single-position A/C/G/T substitutions for sequence strings inside an EDirect-style text pipeline.--- # systematic-mutations Tiny bash filter over `transmute -replace`. It reads `sequence [pattern]` records from stdin, uppercases the sequence, substitutes `A`, `C`, `G`, and `T` at every position, optionally appends the second whitespace-delimited field after a colon, then case-insensitively sorts and deduplicates the emitted variants. ## Quick Start - **Command:** `echo ATGAAACCCGGGTTTTAG | systematic-mutations` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/systematic-mutations` - **Required dependency:** `transmute` on `PATH` ## When To Use This Tool - Generating every single-base substitution of a short sequence - Expanding disambiguated sequence sets into explicit A/C/G/T mutation catalogs - Keeping an attached pattern/label while mutating the leading sequence token - Building small exhaustive mutation sets in a shell pipeline without writing custom code ## Common Patterns ```bash # Enumerate all single-position substitutions echo ATGAAACCCGGGTTTTAG | systematic-mutations ``` ```bash # Preserve a second-column pattern label echo 'ATG tag1' | systematic-mutations ``` ```bash # Expand ambiguous input first, then enumerate mutations echo RCCGGY | disambiguate-nucleotides | systematic-mutations ``` ## Recommended Workflow 1. Feed one sequence per line on stdin, optionally followed by one extra whitespace-delimited label/pattern. 2. Normalize ambiguous bases upstream if you need explicit A/C/G/T inputs before mutation expansion. 3. Pipe the output directly into downstream text filters, because this tool does not create files by itself. 4. Deduplicate or rank the resulting variant strings downstream only if you need more than the built-in case-insensitive uniqueness pass. ## Guardrails - This script ignores command-line flags. Local testing showed `systematic-mutations -h` is silent with no stdin and behaves exactly like the normal mutator when stdin is present. - Input is read from stdin only; the first whitespace-delimited token is the sequence and the second token, if present, is preserved as `:<pattern>`. Additional columns are ignored. - The original sequence can reappear in the output because the substitution loop also tries the existing base at each position before the final `sort -f | uniq -i`. - The script depends on `transmute -replace`; if `transmute` is missing from `PATH`, mutation generation fails.

Frequently asked questions