bio-comparative-genomics-gene-tree-species-tree-reconciliation SKILL.md skillA
bio-comparative-genomics-gene-tree-species-tree-reconciliation 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-gene-tree-species-tree-reconciliation@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-gene-tree-species-tree-reconciliation/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 32,665 bytes
- Repository stars
- 662
- License
- MIT
Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content…
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: ALE 1.0+ (ssolo/ALE github), GeneRax 2.1.3+ (BenoitMorel/GeneRax), AleRax 1.2.0+ (BenoitMorel/AleRax; Morel 2024 Bioinformatics 40:btae162), Whale.jl 2.0+ (arzwa/Whale.jl), RANGER-DTL 2.0+ (Bansal lab; Bansal 2018 Bioinformatics 34:3214), NOTUNG 2.9.1.5+ (Stolzer 2012; Chen 2000), ecceTERA 1.2.5+, Treerecs 1.2+, IQ-TREE 2.3.6+, MrBayes 3.2.7+, BUSCO 5.7+, ete4 4.1.0+, BioPython 1.84+. Open Tree of Life and NCBI Taxonomy reference databases at 2024-Q3 minimum for species-tree-aware inference. Before using code patterns, verify installed versions match. If versions differ: - CLI: `ALEml_undated --help`, `ALEml --help` (dated), `generax --help`, `alerax --help` - Julia: `using Whale; Whale.WhaleProblem`; `]status` for package versions - Python: `pip show ete4`; `ete4 --help` …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-comparative-genomics-gene-tree-species-tree-reconciliation@sha256:230912413f9e6e72The 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_yglixm2pzasfyjbe)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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 (32665 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_yglixm2pzasfyjbe GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-comparative-genomics-gene-tree-species-tree-reconciliation GET https://markdownregistry.com/api/v1/blob/230912413f9e6e72dd724d680e5792e06604ecb5be5edaa7476db10987a48593
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.