Biopython Bioinformatics
aiming-lab/AutoResearchClaw
Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO.
Install Bio Read Sequences
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-sequences --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-read-sequences .claude/skills/bio-read-sequences && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "bio-read-sequences" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences into .claude/skills/bio-read-sequences/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-sequences", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequencesType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-sequences --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-read-sequences .agents/skills/bio-read-sequences && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-read-sequences" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences into .agents/skills/bio-read-sequences/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-sequences", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-sequences --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-read-sequences .cursor/skills/bio-read-sequences && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-read-sequences" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences into .cursor/skills/bio-read-sequences/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-sequences", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-read-sequences--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-sequences --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-read-sequences .gemini/skills/bio-read-sequences && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bio-read-sequences" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences into .gemini/skills/bio-read-sequences/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-sequences", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-sequencesInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-read-sequences .github/skills/bio-read-sequences && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bio-read-sequences" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences into .github/skills/bio-read-sequences/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-sequences", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-read-sequences --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-read-sequences .opencode/skills/bio-read-sequences && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-read-sequences" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences into .opencode/skills/bio-read-sequences/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-read-sequences", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bio-read-sequences- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2.6k tokens
- SKILL.md length
- 658 words
- Files
- 11
- Skills in repo
- 173
- Repo updated
- First seen
- Licence
- None found
At a glance
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO.
- Parsing sequence files
- SKILL.md covers Version Compatibility, Required Import, Core Functions and High-Performance Parsing, plus 7 more sections
- Runs Python scripts from its folder; calls pip
- Iterating multi-sequence files
What it does
Bio Read Sequences is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing.
Its SKILL.md is about 2.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 11 other files (for example `examples/basic_parsing.py`, `examples/fastq_quality.py` and `examples/genbank_features.py`).
It sits in Research & Science, covering Bioinformatics. It works with Biopython, NCBI and SQLite. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Parsing sequence files
- Iterating multi-sequence files
- Random access to large files
- High-performance parsing
Example prompts
- “/bio-read-sequences”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Bio Read Sequences loads about 2.6k tokens when it runs. Until then it costs about 60 tokens; SKILL.md has 658 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 658 words (~2,611 tokens).
“Reference examples tested with: BioPython 1.83+”
- name
- bio-read-sequences
- tool_type
- python
- primary_tool
- Bio.SeqIO
Files
SKILL.md and 10 other files in skills/bio-read-sequences of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/basic_parsing.py
- examples/fastq_quality.py
- examples/genbank_features.py
- examples/random_access.py
- examples/sample.fasta
- examples/sample.fastq
- examples/sample.gb
- examples/single.fasta
- tests.json
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Bio Read Sequences next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Read Sequences this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.6k | Automated safety check: Pass | None | |
| Biopython Bioinformaticsaiming-lab/AutoResearchClaw | 15k | — | ~810 | Automated safety check: Pass | MIT | |
| Bio Write SequencesGPTomics/bioSkills | 1.2k | 3 repos | ~2.1k | Automated safety check: Pass | MIT | |
| Biopythondavila7/claude-code-templates | 32k | 13 repos | ~3.4k | Automated safety check: Pass | MIT | |
| BiopythonK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.3k | Automated safety check: Notes | MIT | |
| Biopythonlamm-mit/scienceclaw | 244 | — | ~3.9k | Automated safety check: Pass | Apache-2.0 |
Similar skills
Bio Write Sequences
GPTomics/bioSkills
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.
Biopython
davila7/claude-code-templates
Primary Python toolkit for molecular biology. An agent skill from davila7/claude-code-templates.
Biopython
K-Dense-AI/scientific-agent-skills
Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez).
Biopython
lamm-mit/scienceclaw
Computational molecular biology library (sequence I/O, alignment, phylogenetics).
Tooluniverse Phylogenetics
wu-yc/LabClaw
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.
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Related
Categories
Questions about Bio Read Sequences
What does Bio Read Sequences do?
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Bio Read Sequences is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.SeqIO.
When should I use Bio Read Sequences?
Bio Read Sequences fits situations like: parsing sequence files; iterating multi-sequence files; random access to large files; high-performance parsing.
How do I install Bio Read Sequences in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a claude-code`. Or copy the skill folder (skills/bio-read-sequences in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-read-sequences in your project. Claude Code loads it when a task matches its description.
How do I install Bio Read Sequences in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a codex`. Or copy the skill folder (skills/bio-read-sequences in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-read-sequences in your project. Codex loads it when a task matches its description.
Can I use Bio Read Sequences in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-read-sequences, .gemini/skills/bio-read-sequences, .github/skills/bio-read-sequences and .opencode/skills/bio-read-sequences in your project.
What does Bio Read Sequences need to run?
Going by SKILL.md and its folder, Bio Read Sequences needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Read Sequences access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Read Sequences safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Bio Read Sequences use?
No licence was found for Bio Read Sequences or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Read Sequences use?
About 2.6k tokens (SKILL.md is roughly 10k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bio Read Sequences?
Skills that share tags, products or a category with Bio Read Sequences: Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars), Biopython (davila7/claude-code-templates, 32k stars) and Biopython (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Read Sequences?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.