phylogenetics
Automates the reconstruction and analysis of evolutionary history using MAFFT, IQ-TREE 2, and FastTree.
Install
mkdir -p .claude/skills/phylogenetics && curl -L -o skill.zip "https://agentskills.codes/api/skills/download/11747" && unzip -o skill.zip -d .claude/skills/phylogenetics && rm skill.zipInstalls to .claude/skills/phylogenetics
Activation
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Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.Key capabilities
- →Perform multiple sequence alignment with MAFFT
- →Build maximum likelihood phylogenetic trees with IQ-TREE 2
- →Build fast approximate maximum likelihood trees with FastTree
- →Manipulate and visualize trees with ETE3
- →Trim poorly aligned columns with TrimAl
- →Select appropriate models for DNA and protein sequences
How it works
The skill processes biological sequences by first aligning them with MAFFT, then inferring phylogenetic trees using IQ-TREE 2 or FastTree, and finally allows for tree manipulation and visualization with ETE3.
Inputs & outputs
When to use phylogenetics
- →Aligning multiple protein or DNA sequences
- →Inferring evolutionary relationships between organisms
- →Tracing viral transmission dates
- →Reconstructing ancestral protein sequences
About phylogenetics
Processes biological sequences to infer branching patterns of descent. It integrates multiple alignment tools and tree inference algorithms to facilitate evolutionary, protein family, and viral phylodynamic analysis.
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
When not to use it
- →When analyzing single-variant GWAS
- →When performing variant prioritization for clinical interpretation
- →When detecting recombination in viral/bacterial sequences before tree building
Prerequisites
Limitations
- →Poor alignment leads to unreliable trees.
- →IQ-TREE becomes slow for datasets larger than 5000 sequences.
- →Trees should be rooted using an outgroup or midpoint rooting.
How it compares
This skill provides a complete pipeline for phylogenetic analysis from sequence alignment to tree visualization, unlike using individual tools separately without integrated guidance.
Compared to similar skills
phylogenetics side by side with the closest alternatives in the catalog.
| Skill | Installs | Updated | Safety | Difficulty |
|---|---|---|---|---|
| phylogenetics (this skill) | 0 | 4mo | Review | Advanced |
| exploratory-data-analysis | 15 | 3mo | Review | Intermediate |
| model-compare | 7 | 9mo | Review | Advanced |
| astropy | 6 | 9mo | Review | Advanced |
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