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-comparative-genomics-ancestral-reconstructiongit 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-comparative-genomics-ancestral-reconstruction)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-comparative-genomics-ancestral-reconstruction"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-ancestral-reconstruction/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-comparative-genomics-ancestral-reconstruction"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-ancestral-reconstruction.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 | $0.00149 | $0.09772 |
| Opus 5 | $0.00075 | $0.04886 |
| Sonnet 5 | $0.00030 | $0.01954 |
| Haiku 4.5 | $0.00015 | $0.00977 |
Grade A, and why
bio-comparative-genomics-ancestral-reconstruction 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 9d 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-comparative-genomics-ancestral-reconstruction — 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 — 484 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: PAML 4.10.7+, IQ-TREE 2.3.6+, GRASP 2024+ (web/CLI), FastML 3.11+, RevBayes 1.2.4+, BayesTraits V4.1+, R 4.4+, ape 5.8+, phytools 2.3+, corHMM 2.9+, geiger 2.0.11+, phangorn 2.12+, RERconverge 0.3.0+, BioPython 1.84+.
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('corHMM')then?ancRECON,?make.simmap,?ace - CLI:
codeml(no--version; checkpaml -hor examinePhylip.treexample),iqtree2 --version,revbayes --version - Python:
pip show biopython; checkBio.Phylo.PAML.codemlAPI
If code throws AttributeError, ImportError, missing slot errors on R S4 objects, or PAML mlc parsing failures, introspect the installed package (? in R, help() in Python) and adapt the example rather than retrying. PAML output formats are stable across 4.9 -> 4.10; IQ-TREE's --ancestral flag replaced -asr in v2.0+.
Ancestral State Reconstruction
"What did this gene / trait / genome look like at an internal node?" -> Choose the reconstruction framework that matches the data class (sequence / discrete trait / continuous trait / gene content) and the inference question (point estimate vs full posterior; marginal vs joint vs scaled-conditional). The single most common mistake is reconstructing under a site-independent or trait-stationary model when the underlying biology demands a hidden-rate or epistatic model -- the resulting "ancestor" is mathematically optimal under the wrong model and is silently wrong (Beaulieu & O'Meara 2016 Syst Biol 65:583; Boyko & Beaulieu 2021 MEE 12:468).
- Sequence ASR (protein resurrection): PAML codeml
RateAncestor=1; IQ-TREE2--ancestral; GRASP (graph-based, handles indels); FastML (Bayesian) - Discrete traits: R
ape::ace(type='discrete');corHMM::corHMM()(rate categories);phytools::make.simmap()stochastic mapping; BayesTraits MultiState/Discrete - Continuous traits:
phytools::fastAnc();phytools::contMap();geiger::fitContinuous(model='BM'|'OU'|'EB'); RPANDAfit_t_env() - Ancestral gene content (presence/absence):
ape::ace(type='discrete', model='ARD'); Dollo parsimony in phangorn; ALE/GeneRax for full DTL (see [[gene-tree-species-tree-reconciliation]])
What ships with it
2 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.
- 9d ago First seen · 484 lines · 149 tokens per session scan A 80b571f837a1
bio-comparative-genomics-ancestral-reconstruction is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 149 tokens to every session and 9,772 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to bio-comparative-genomics-ancestral-reconstruction, differing in 12 lines, and is treated as a copy.
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