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phylogenetics

Build and analyze phylogenetic trees with MAFFT, IQ-TREE 2, and FastTree.

13|3|Updated Jun 10, 2026
Search Tags:#evolutionary biology#phylogenetics#sequence alignment#tree inference#tree visualization
One-click install
npx skills add https://github.com/tassiovale/claude-code-kit --skill phylogenetics-tassiovale
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/phylogenetics
Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill phylogenetics-tassiovale

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires mafft, iqtree2, fasttree, ete3, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the complex process of building and analyzing phylogenetic trees, providing accurate and efficient analysis for evolutionary biology research.

Core Features & Use Cases

  • Phylogenetic Tree Building: Automatically constructs phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree.
  • Data Alignment: Performs multiple sequence alignment with MAFFT for reliable tree construction.
  • Tree Inference: Inferences the most likely tree topology using maximum likelihood methods with IQ-TREE 2 and fast approximate methods with FastTree.
  • Visualization: Visualizes trees with ETE3 for detailed analysis and presentation.
  • Use Case: For researchers working on microbial genomics, viral phylodynamics, or protein family analysis, this Skill can streamline the process of inferring evolutionary relationships and estimating divergence times.

Quick Start

Use the phylogenetics skill to build a phylogenetic tree from the aligned sequences in 'sequences.fasta'.

Frequently Asked Questions about phylogenetics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I build a phylogenetic tree from a FASTA file?▼

To build a phylogenetic tree, this process performs multiple sequence alignment with MAFFT, infers tree topology using IQ-TREE 2 or FastTree, and visualizes the result with ETE3.

What is the best way to automate multiple sequence alignment and tree inference for microbial genomics?▼

Automating multiple sequence alignment and tree inference for microbial genomics is handled by chaining MAFFT for alignment, IQ-TREE 2 for maximum likelihood tree inference, and ETE3 for visualization.

Do I need MAFFT and IQ-TREE 2 installed to infer maximum likelihood phylogenetic trees?▼

Yes, you need MAFFT, IQ-TREE 2, FastTree, and ETE3 installed locally to perform the multiple sequence alignment, maximum likelihood tree inference, and tree visualization.

Can I use FastTree for fast approximate tree inference instead of IQ-TREE 2?▼

Yes, FastTree provides fast approximate phylogenetic tree inference, while IQ-TREE 2 is used for more rigorous maximum likelihood tree topology estimation.

Why use ETE3 for phylogenetic tree visualization?▼

ETE3 is used for phylogenetic tree visualization to provide detailed analysis and presentation of the inferred evolutionary relationships and divergence times.

Does this approach work for viral phylodynamics and protein family analysis?▼

Yes, this phylogenetic tree building and analysis process applies directly to evolutionary biology research, including viral phylodynamics, microbial genomics, and protein family analysis.

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