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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-phylo-modern-tree-inference
Maintainer FreedomIntelligence · Last updated April 1, 2026
Maximum likelihood tree inference with IQ-TREE 2 or FastTree.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-phylo-modern-tree-inference
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Build maximum likelihood phylogenetic trees with automatic model selection and ultrafast bootstrap.
- iqtree2 -s alignment.fasta -m MFP -B 1000 -T AUTO.
Source Doc
Excerpt From SKILL.md
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 |
ModelFinder only (no tree inference)
iqtree2 -s alignment.fasta -m MF
Use specific model
iqtree2 -s alignment.fasta -m GTR+G4 -B 1000
Use cases
- Use bio-phylo-modern-tree-inference for genomics and bioinformatics workflows.
- Apply bio-phylo-modern-tree-inference to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- tree-io - Read and convert output tree files
- tree-visualization - Visualize trees with bootstrap support
- distance-calculations - Compare with distance-based methods
- alignment/alignment-io - Prepare alignments for tree inference
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