bio-alignment-io skillA
bio-alignment-io is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-io@sha256:67a0077a163a5206Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_zr32tbhyag6cglah)
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Versions
Audit of the latest version
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- pass: Frontmatter declares a name
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- 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 · 586 stars · license MIT · pushed 2026-09-23 · 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
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