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phylogenetics

Automate phylogenetic tree building and analysis with MAFFT, IQ-TREE, and FastTree.

Updated May 8, 2026
Search Tags:#evolutionary biology#phylogenetics#tree analysis#sequence alignment#tree building
One-click install
npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill phylogenetics-zeyuyang-0420
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/Zeyuyang-0420/bio-ai-research-skills/tree/main/categories/bioinformatics-genomics/phylogenetics
Command: npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill phylogenetics-zeyuyang-0420

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the process of building and analyzing phylogenetic trees, which is essential for evolutionary biology, microbial genomics, and viral phylodynamics.

Core Features & Use Cases

  • Phylogenetic Tree Building: Align sequences, build trees using MAFFT, IQ-TREE, and FastTree.
  • Tree Analysis: Analyze tree statistics, compute distances, and find the most recent common ancestor.
  • Visualization: Visualize trees with ETE3 and FigTree.
  • Use Case: For a researcher studying the evolutionary history of a viral strain, this Skill can automate the process of aligning sequences, building a phylogenetic tree, and visualizing the results.

Quick Start

Run the phylogenetic analysis pipeline on the provided sequences with the following command:

python scripts/phylogenetic_analysis.py sequences.fasta --type nt --threads 4

Frequently Asked Questions about phylogenetics

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

FAQPage Schema
How do I automate phylogenetic tree building from sequence alignments?▼

You can automate phylogenetic tree building by running a Python script that utilizes MAFFT for sequence alignment, followed by IQ-TREE or FastTree to construct the phylogenetic tree from your FASTA sequences.

Can I use IQ-TREE and FastTree for viral phylodynamics and microbial genomics?▼

Yes, IQ-TREE and FastTree are fully supported for building phylogenetic trees, making the pipeline suitable for evolutionary biology, microbial genomics, and viral phylodynamics sequence analysis.

What is the best way to visualize phylogenetic trees and compute evolutionary distances?▼

The best way to visualize phylogenetic trees and compute evolutionary distances is using ETE3 and FigTree, which analyze tree statistics and find the most recent common ancestor.

Do I need Python libraries like ete3 and mafft installed to run phylogenetic analysis?▼

Yes, you need Python libraries including ete3, mafft, iqtree2, and fasttree installed in your environment to execute the automated phylogenetic analysis pipeline successfully.

How to analyze tree statistics and find the most recent common ancestor?▼

To analyze tree statistics and find the most recent common ancestor, execute the phylogenetic pipeline which processes aligned sequences and outputs visualizations using ETE3.

Does the phylogenetic pipeline support nucleotide sequence alignment in FASTA format?▼

Yes, the phylogenetic pipeline supports nucleotide sequence alignment in FASTA format, allowing you to specify the sequence type and allocate multiple threads for processing.

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