bio-alignment-io SKILL.md skillA
bio-alignment-io from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-alignment-io@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-alignment-alignment-io/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 19,978 bytes
- Repository stars
- 662
- License
- MIT
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Alignment File I/O Read, write, and convert multiple sequence alignment files in various formats. ## Required Import **Goal:** Load modules for reading, writing, and manipulating multiple sequence alignments. **Approach:** Import AlignIO for file I/O and supporting classes for programmatic alignment construction. ```python from Bio import AlignIO from Bio.Align import MultipleSeqAlignment from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq ``` ## Format Coverage Map Three Python libraries cover the alignment-format space, with overlapping but non-identical support. Pick by what is actually required. | Format | `Bio.AlignIO` | `Bio.Align` (modern) | `pyhmmer.easel` | Notes | |--------|---------------|----------------------|-----------------|-------| …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-io@sha256:67a0077a163a5206The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_zr32tbhyag6cglah)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (19978 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zr32tbhyag6cglah GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-io GET https://markdownregistry.com/api/v1/blob/67a0077a163a52062ea1d1e469dc64382e597642d5e83e1c5b247dd550030893
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
More from pku-yuangroup/openai4s
Every file in pku-yuangroup/openai4s