etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
73
66%
Does it follow best practices?
Impact
85%
1.37xAverage score across 3 eval scenarios
Passed
No known issues
Optimize this skill with Tessl
npx tessl skill review --optimize ./scientific-skills/etetoolkit/SKILL.mdEvaluation results
64%
50%Phylogenetic Tree Preprocessing Pipeline
Tree format conversion and preprocessing pipeline
uv installation
0%
0%
Newick format on read
0%
100%
Newick format on write
0%
100%
Preserve branch length
0%
100%
Midpoint rooting
0%
100%
Resolve polytomies
0%
100%
Iterator usage
0%
0%
Script usage
0%
0%
Stats subcommand
0%
0%
Output files produced
100%
100%
Process log
100%
100%
100%
8%Gene Family Ortholog Identification
Gene tree evolutionary event analysis
PhyloTree import
100%
100%
Species naming function
100%
100%
Evol events detection
100%
100%
Duplication nodes identified
100%
100%
Speciation nodes identified
100%
100%
Ortholog extraction
100%
100%
Ortholog files saved
100%
100%
uv installation
0%
100%
Results summary
100%
100%
Orthologs for query gene
100%
100%
92%
10%Phylogenetic Figure for a Mammal Systematics Paper
Publication-quality tree visualization
PDF or SVG output
100%
100%
TreeStyle used
100%
100%
NodeStyle applied
100%
100%
Layout function
100%
100%
Support-based coloring
100%
100%
Face elements added
100%
100%
quick_visualize script
0%
100%
uv installation
0%
0%
show_branch_support
100%
100%
Scale parameter
100%
100%
- Repository
- K-Dense-AI/claude-scientific-skills
- Commit
b58ad7e
- Evaluated
- Agent
- Claude Code
- Model
- Claude Sonnet 4.6
Table of Contents
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