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 thesecondfox/skill --skill bio-phylogenetics-modern-tree-inferencegit clone --depth 1 https://github.com/thesecondfox/skillWrote 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/thesecondfox/skill/bio-phylogenetics-modern-tree-inference)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-phylogenetics-modern-tree-inference"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-phylogenetics-modern-tree-inference.svg" alt="Measured on agentmods" 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 | $0.00052 | $0.02259 |
| Opus 5 | $0.00026 | $0.01130 |
| Sonnet 5 | $0.00010 | $0.00452 |
| Haiku 4.5 | $0.00005 | $0.00226 |
Grade A, and why
bio-phylo-modern-tree-inference 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 4d 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.
How it starts
The opening of the file, as written. The whole thing — 269 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: IQ-TREE 2.2+
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Modern ML Tree Inference
"Infer a maximum likelihood tree from my alignment" → Build publication-quality ML trees with automatic substitution model selection and ultrafast bootstrap support assessment.
- CLI:
iqtree2 -s alignment.fa -m MFP -B 1000(IQ-TREE2) - CLI:
raxml-ng --all --msa alignment.fa --model GTR+G --bs-trees 100(RAxML-ng)
Build maximum likelihood phylogenetic trees with automatic model selection and ultrafast bootstrap.
IQ-TREE2 Basic Usage
# Simple ML tree with automatic model selection
iqtree2 -s alignment.fasta -m MFP -B 1000 -T AUTO
# -s: input alignment
# -m MFP: ModelFinder Plus (automatic model selection + tree inference)
# -B 1000: 1000 ultrafast bootstrap replicates (minimum recommended for publication)
# -T AUTO: automatic thread detection
IQ-TREE2 Output Files
| File | Description |
|---|---|
.treefile |
Best ML tree in Newick format |
.iqtree |
Full analysis report with model parameters |
.log |
Run log |
.contree |
Consensus tree with bootstrap support |
.splits.nex |
Bootstrap splits in Nexus format |
.model.gz |
Model parameters |
.bionj |
Initial BIONJ tree |
.mldist |
ML distance matrix |
.ckp.gz |
Checkpoint file for resuming |
Model Selection
# ModelFinder only (no tree inference)
iqtree2 -s alignment.fasta -m MF
# Use specific model
iqtree2 -s alignment.fasta -m GTR+G4 -B 1000
# Test only specific models
iqtree2 -s alignment.fasta -m MF -mset GTR,HKY,K2P
# Protein models
iqtree2 -s protein.fasta -m MFP -B 1000 -st AA
Common DNA Substitution Models
| Model | Parameters | Use Case |
|---|---|---|
| JC | Equal rates | Very simple, rarely appropriate |
| K2P/K80 | Ti/Tv ratio | Simple, some rate variation |
| HKY | Ti/Tv + base freq | Moderate complexity |
| GTR | 6 rates + base freq | Most general, recommended default |
| +G4 | Gamma rate variation | 4 discrete rate categories |
| +I | Invariant sites | Sites that never change |
| +R4 | FreeRate model | More flexible than Gamma |
What ships with it
1 file 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.
- 4d ago First seen · 269 lines · 52 tokens per session scan A d2b8746ee522
bio-phylo-modern-tree-inference is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 52 tokens to every session and 2,259 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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