How do I install the Bioinformatics Toolkit skill?

Run npx skillmds add vimalinx/bioinformatics-toolkit 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 Bioinformatics Toolkit safe to use?

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

Which AI agents work with Bioinformatics Toolkit?

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 Bioinformatics Toolkit free to use?

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

Who published Bioinformatics Toolkit?

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

Bioinformatics Toolkit by vimalinx — Agent Skill

Name: Bioinformatics Toolkit
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

bioinformatics-toolkit

Top-level workspace gateway for bioinformatics work. In this environment, the most reliable local assets are the bio conda env CLIs (blast*, bowtie2, bwa, samtools, bcftools, prodigal, RNAfold, iqtree, hmmscan, mafft, muscle, hisat2, featureCounts, seqkit) plus several repo-backed projects under repositories/active/ such as Biomni, evo2, and RFdiffusion.

Quick Start

Activate environment: conda activate bio
Verified local CLI families: BLAST, Bowtie2, BWA, Samtools, Bcftools, HMMER, MAFFT, MUSCLE, Prodigal, ViennaRNA, IQ-TREE, SeqKit
Repo-backed projects: /home/vimalinx/Projects/bio_studio/repositories/active/Biomni, /home/vimalinx/Projects/bio_studio/repositories/active/evo2, /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion

When To Use This Tool

Figuring out which local tool family or project should handle a bioinformatics request
Starting from a workspace-wide inventory instead of guessing what is installed
Routing between plain CLIs, teaching projects, and heavier repo-backed AI workflows
Auditing whether a proposed method matches the actual assets in this workspace

Common Patterns

# Check the core local CLI toolchain
command -v blastn bowtie2 bwa samtools bcftools prodigal RNAfold iqtree

# Start a classic alignment + BAM-processing workflow
bowtie2 -x ref_index -U reads.fq -S aligned.sam
samtools view -bS aligned.sam | samtools sort -o aligned.sorted.bam

# Start an RNA structure or phylogeny workflow
RNAfold < sequences.fa
iqtree -s alignment.fa

# Inspect repo-backed bio projects
ls /home/vimalinx/Projects/bio_studio/repositories/active

Recommended Workflow

Begin with the verified CLI inventory in the bio environment.
Route the task to a narrower skill whenever the job has a clear domain: sequence analysis, protein structure/design, yeast learning project, Biomni, Evo 2, or RFdiffusion.
Use repo-backed projects only after confirming their extra dependencies are satisfied.
Keep the umbrella skill focused on tool selection and environment reality checks, not on pretending every downstream project is already turnkey.

Guardrails

The reliable base layer here is the installed CLI toolchain in the bio environment.
Repo-backed projects like Biomni, Evo 2, and RFdiffusion are present locally but each has additional setup gaps or missing dependencies.
Do not advertise absent tools just because earlier autogenerated docs mentioned them. Limit recommendations to commands or repos that are actually present.
When in doubt, prefer the narrower skill that matches the concrete subtask.

---name: bioinformatics-toolkitdescription: Use when you need a workspace-level entry point to choose among the installed bioinformatics CLIs and repo-backed AI/bio projects in this environment.--- # bioinformatics-toolkit Top-level workspace gateway for bioinformatics work. In this environment, the most reliable local assets are the `bio` conda env CLIs (`blast*`, `bowtie2`, `bwa`, `samtools`, `bcftools`, `prodigal`, `RNAfold`, `iqtree`, `hmmscan`, `mafft`, `muscle`, `hisat2`, `featureCounts`, `seqkit`) plus several repo-backed projects under `repositories/active/` such as `Biomni`, `evo2`, and `RFdiffusion`. ## Quick Start - **Activate environment:** `conda activate bio` - **Verified local CLI families:** BLAST, Bowtie2, BWA, Samtools, Bcftools, HMMER, MAFFT, MUSCLE, Prodigal, ViennaRNA, IQ-TREE, SeqKit - **Repo-backed projects:** `/home/vimalinx/Projects/bio_studio/repositories/active/Biomni`, `/home/vimalinx/Projects/bio_studio/repositories/active/evo2`, `/home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion` ## When To Use This Tool - Figuring out which local tool family or project should handle a bioinformatics request - Starting from a workspace-wide inventory instead of guessing what is installed - Routing between plain CLIs, teaching projects, and heavier repo-backed AI workflows - Auditing whether a proposed method matches the actual assets in this workspace ## Common Patterns ```bash # Check the core local CLI toolchain command -v blastn bowtie2 bwa samtools bcftools prodigal RNAfold iqtree ``` ```bash # Start a classic alignment + BAM-processing workflow bowtie2 -x ref_index -U reads.fq -S aligned.sam samtools view -bS aligned.sam | samtools sort -o aligned.sorted.bam ``` ```bash # Start an RNA structure or phylogeny workflow RNAfold < sequences.fa iqtree -s alignment.fa ``` ```bash # Inspect repo-backed bio projects ls /home/vimalinx/Projects/bio_studio/repositories/active ``` ## Recommended Workflow 1. Begin with the verified CLI inventory in the `bio` environment. 2. Route the task to a narrower skill whenever the job has a clear domain: sequence analysis, protein structure/design, yeast learning project, Biomni, Evo 2, or RFdiffusion. 3. Use repo-backed projects only after confirming their extra dependencies are satisfied. 4. Keep the umbrella skill focused on tool selection and environment reality checks, not on pretending every downstream project is already turnkey. ## Guardrails - The reliable base layer here is the installed CLI toolchain in the `bio` environment. - Repo-backed projects like Biomni, Evo 2, and RFdiffusion are present locally but each has additional setup gaps or missing dependencies. - Do not advertise absent tools just because earlier autogenerated docs mentioned them. Limit recommendations to commands or repos that are actually present. - When in doubt, prefer the narrower skill that matches the concrete subtask.

Frequently asked questions