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 GPTomics/bioSkills --skill gene-tree-species-tree-reconciliationgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/gene-tree-species-tree-reconciliation)<a href="https://agentmods.dev/skills/gptomics/bioskills/gene-tree-species-tree-reconciliation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/gene-tree-species-tree-reconciliation/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/gptomics/bioskills/gene-tree-species-tree-reconciliation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/gene-tree-species-tree-reconciliation.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 | $0.00190 | $0.08362 |
| Opus 5 | $0.00095 | $0.04181 |
| Sonnet 5 | $0.00038 | $0.01672 |
| Haiku 4.5 | $0.00019 | $0.00836 |
Grade A, and why
bio-comparative-genomics-gene-tree-species-tree-reconciliation scanned grade A with 1 finding 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 8d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget https://compbio.engr.uconn.edu/software/RANGER-DTL/RANGER-DTL-Linux.tar.gz Copies of this mod
1 near-identical copy found in the catalogue:
- bio-comparative-genomics-gene-tree-species-tree-reconciliation — 94% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 493 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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;]statusfor package versions - Python:
pip show ete4;ete4 --help
If code throws species tree mismatch, gene tree taxa not in species tree, or MPI process pool failure, these reconciliation tools share strict label-consistency requirements: species labels must match exactly across the species tree and gene trees (case-sensitive, no whitespace), and gene IDs typically encode species via prefix (species|gene_id separator convention). Use sed / awk normalization scripts before reconciliation.
Gene Tree Species Tree Reconciliation
"Where did this gene family come from, and what events shaped its history?" -> Reconcile gene trees against species trees under explicit probabilistic models of duplication (D), horizontal transfer (T), and loss (L). The reconciliation framework converts gene-tree-species-tree discordance into a quantitative history of evolutionary events. Modern probabilistic methods (ALE, GeneRax, AleRax) distinguish gene-tree-error-driven discordance from biological discordance by integrating over gene-tree uncertainty -- a critical advance over parsimony reconciliation (NOTUNG, RANGER) which treats input gene trees as fixed and inflates duplication/loss counts from gene-tree noise (Boussau 2013 Genome Res 23:323; Morel 2020 MBE 37:2763).
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.
- 8d ago First seen · 493 lines · 190 tokens per session scan A 599f0aee5c5f
bio-comparative-genomics-gene-tree-species-tree-reconciliation is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 190 tokens to every session and 8,362 once invoked, about $0.0010 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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