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phylogenetics

Infer evolutionary relationships from nucleotide or protein sequences using MAFFT, IQ-TREE 2, and ETE3.

1|Updated Mar 19, 2026
Search Tags:#visualization#alignment#MAFFT#phylogenetics#IQ-TREE#tree-inference#FastTree
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill phylogenetics-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/phylogenetics
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill phylogenetics-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Reconstructs evolutionary history by building and analyzing phylogenetic trees from biological sequences, enabling researchers to infer relationships among organisms, genes, or proteins.

Core Features & Use Cases

  • End-to-end workflow: from multiple sequence alignment (MAFFT) to tree inference (IQ-TREE 2 or FastTree) and visualization (ETE3 or FigTree).
  • Flexible models & bootstrapping: supports model testing, ultrafast bootstrap, and Outgroup rooting for robust trees.
  • Use Case: explore viral phylogenetics, microbial genomics, and protein family evolution with scalable pipelines.

Quick Start

Run a basic phylogenetic analysis by supplying an unaligned FASTA file to generate an inferred tree and a visualization.

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 an unaligned FASTA file?▼

To build a phylogenetic tree from an unaligned FASTA file, this workflow runs MAFFT for sequence alignment, then IQ-TREE 2 or FastTree for inference, and ETE3 or FigTree for visualization.

What's the best way to infer evolutionary relationships from viral sequences?▼

Infer evolutionary relationships from viral sequences by constructing phylogenetic trees using model testing, ultrafast bootstrap support, and optional outgroup rooting for robust viral phylodynamics analysis.

Does IQ-TREE 2 support ultrafast bootstrap and model testing for phylogenetics?▼

Yes, IQ-TREE 2 supports ultrafast bootstrap and model testing for phylogenetics. The workflow applies these features to produce robust evolutionary trees with statistically supported branches.

Can I use MAFFT for multiple sequence alignment before tree inference?▼

Yes, you can use MAFFT for multiple sequence alignment before tree inference. It serves as the starting point of the workflow, taking raw nucleotide or protein sequences and generating aligned input.

How do I visualize a phylogenetic tree after inference?▼

To visualize a phylogenetic tree after inference, use ETE3 or FigTree. Both tools render the inferred tree structures, allowing you to analyze evolutionary relationships graphically.

What are the limitations of FastTree compared to IQ-TREE 2 for tree inference?▼

FastTree offers faster tree inference for large datasets, while IQ-TREE 2 provides extensive model testing and ultrafast bootstrap. Choose FastTree for speed or IQ-TREE 2 for rigorous statistical support.

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