Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-alignment-alignment-trimminggit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-alignment-trimming)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-alignment-trimming"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-alignment-trimming/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-alignment-trimming"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-alignment-trimming.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00060 | $0.06053 |
| Opus 5 | $0.00030 | $0.03027 |
| Sonnet 5 | $0.00012 | $0.01211 |
| Haiku 4.5 | $0.00006 | $0.00605 |
Grade A, and why
bio-alignment-trimming scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
97% identical to bio-alignment-trimming — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 319 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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>thenhelp(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.
Tool choice and aggressiveness matter more than trimming vs not-trimming. Pick a mode by dataset character (table below), and always run a sensitivity check by building trees on trimmed and untrimmed alignments.
Pick a Trimming Mode by Dataset Character
| Dataset character | Trimming effect | Recommended approach |
|---|---|---|
| Deep-divergence orthologs (>500 Ma), saturated 3rd codons | Aggressive trimming HURTS (Tan-style result) | No trim or kpic-smart-gap only; report sensitivity to trimming choice |
| Mid-depth eukaryotic (animal phyla, fungal classes) | ClipKIT kpic-smart-gap HELPS |
Steenwyk-style result |
| Shallow (within-genus) | All trimmers ~equivalent | Choose for downstream-tool compatibility |
| Concatenated supermatrix with very long alignments (>10 kb) | Trimming reduces phylogenetic noise | kpic-smart-gap or BMGE -h 0.5 |
| Single short genes (<200 bp aligned) | Trimming amplifies stochastic error | Skip column trimming; use sequence-level outlier filtering |
What ships with it
5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 11d ago First seen · 319 lines · 60 tokens per session scan A 6328149f4bd5
bio-alignment-trimming is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (403 stars, last pushed today), licensed MIT. It adds 60 tokens to every session and 6,053 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to bio-alignment-trimming, differing in 12 lines, and is treated as a copy.
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