bio-alignment-trimming skillA
bio-alignment-trimming is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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: 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. …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-trimming@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-trimming@sha256:6328149f4bd528adPin 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_o67o4rtn56bmtml5)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · 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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