bio-alignment-multiple SKILL.md skillA
bio-alignment-multiple 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-multiple@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-multiple-alignment/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 33,984 bytes
- Repository stars
- 662
- License
- MIT
Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
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: MAFFT 7.520+, MUSCLE 5.1+, ClustalOmega 1.2.4+, T-Coffee 13+, PAL2NAL 14+, BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `mafft --version`, `muscle -version`, `clustalo --version` - Python: `pip show biopython` then `help(module.function)` to check signatures If code throws errors, introspect the installed tool and adapt the example to match the actual CLI flags rather than retrying. # Multiple Sequence Alignment **"Align multiple sequences"** -> Compute an optimal alignment of three or more homologous sequences using progressive, iterative, or consistency-based methods. - CLI: `mafft` (most versatile), `muscle` (highest accuracy), `clustalo` (scales well), `t_coffee` (consistency-based) - Python: `subprocess.run()` wrapping CLI tools; BioPython `Bio.Align.Applications` was removed in BioPython 1.86 (verify with `pip show biopython`); use `subprocess` directly ## MSA Algorithm Taxonomy When a tool is failing on a dataset, switch to a tool from a different algorithmic family rather than tuning flags. The six families and their characteristic failure modes: …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-multiple@sha256:ff8a8f6274ce33f1The 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_lfyynuf3cv5o5zfq)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_lfyynuf3cv5o5zfq GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-multiple GET https://markdownregistry.com/api/v1/blob/ff8a8f6274ce33f1e1e6eb4e9afb6a0b78b95f6d77d7572b4ce0546f3e257c4e
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.