bio-alignment-trimming SKILL.md skillA
bio-alignment-trimming 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-trimming@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-trimming/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 23,972 bytes
- Repository stars
- 662
- License
- MIT
Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
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: ClipKIT 2.1+, trimAl 1.4+, BMGE 1.12+, Divvier 1.01+, HMMcleaner (current CPAN release of `Bio::MUST::Apps::HmmCleaner`), BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `clipkit --version`, `trimal --version`, `BMGE --help`, `Divvier --help` - 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 Trimming **"Remove unreliable columns from this MSA"** -> Filter or split columns based on gap fraction, conservation, entropy, or per-residue quality. - CLI: `clipkit`, `trimal`, `BMGE`, `Divvier`, `HMMcleaner` - Python: post-process via Bio.AlignIO with custom column masks **"Make this alignment publication-grade for phylogenetics"** -> Apply ClipKIT's `kpic-smart-gap` mode, or trimAl `-automated1`, then verify via tree-stability comparison before vs after trimming. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-trimming@sha256:6328149f4bd528adThe 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_o67o4rtn56bmtml5)
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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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- 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
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- 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_o67o4rtn56bmtml5 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-trimming GET https://markdownregistry.com/api/v1/blob/6328149f4bd528ada62a2ba9d5402dc83d34c86235f0137f8c5a2d307b37b9b8
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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.
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