bio-comparative-genomics-ancestral-reconstruction SKILL.md skillA
bio-comparative-genomics-ancestral-reconstruction 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-comparative-genomics-ancestral-reconstruction@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-comparative-genomics-ancestral-reconstruction/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 37,203 bytes
- Repository stars
- 638
- License
- MIT
Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution…
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: 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`; check `paml -h` or examine `Phylip.tre` example), `iqtree2 --version`, `revbayes --version`
- Python: `pip show biopython`; check `Bio.Phylo.PAML.codeml` API
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
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-comparative-genomics-ancestral-reconstruction@sha256:80b571f837a15920The 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_zzmh6zpufhssrbiy)
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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 zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- 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
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Source
pku-yuangroup/openai4s · 638 stars · license MIT · pushed 2026-10-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zzmh6zpufhssrbiy GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-comparative-genomics-ancestral-reconstruction GET https://markdownregistry.com/api/v1/blob/80b571f837a15920ebf855287bfeef3bfc003d8336ccd55f3b4d2f67014c21ab
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.
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