bio-comparative-genomics-ancestral-reconstruction SKILL.md skillA
bio-comparative-genomics-ancestral-reconstruction from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-comparative-genomics-ancestral-reconstruction@git:20260726.5bc48c3Pins git:20260726.5bc48c3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/ancestral-reconstruction/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260726.5bc48c3, committed Jul 26, 2026
- First version recorded
- May 20, 2026
- Size
- 36,963 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
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 fridrichmethod/awesome-skills/bio-comparative-genomics-ancestral-reconstruction@sha256:b6b72971d3b53468The line at the top of this page pins the label git:20260726.5bc48c3, 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_op5etcnxc5ea7tmk)
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Versions
The registry has recorded 5 versions of this file, between May 20, 2026 and Jul 26, 2026, about one every 17 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260726.5bc48c3 latest | 2026-07-26 | 5bc48c3 | 36,963 B | A | view · diff |
| git:20260705.1380472 | 2026-07-05 | 1380472 | 36,737 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 36,703 B | A | view · diff |
| git:20260528.89ddef6 | 2026-05-28 | 89ddef6 | 36,706 B | A | view · diff |
| git:20260520.e1c72b6 | 2026-05-20 | e1c72b6 | 36,689 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (36963 bytes)
- 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
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_op5etcnxc5ea7tmk GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-comparative-genomics-ancestral-reconstruction GET https://markdownregistry.com/api/v1/blob/b6b72971d3b5346807eff3edcb3ce84e5231df37a9c8a3afb45fc7537d231ae1
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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