phylogenetics

Reconstruct evolutionary relationships via sequence alignment, tree inference, and visualization.

2|Updated Jun 4, 2026

Search Tags:#bioinformatics #genomics #evolutionary biology #phylogenetics #sequence alignment #tree inference

Ready to run

npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill phylogenetics-lord1egypt

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/Lord1Egypt/scientific-agent-toolkit/tree/main/scientific-skills/phylogenetics
Command: npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill phylogenetics-lord1egypt

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This skill streamlines the complex, multi-step process of reconstructing evolutionary histories from biological sequences, reducing the risk of manual errors and inconsistent methodology.

Core Features & Use Cases

End-to-End Pipeline: Automates the entire workflow from multiple sequence alignment to tree inference and visualization.
Flexible Inference: Supports both high-accuracy maximum likelihood inference via IQ-TREE 2 and high-speed approximate inference via FastTree for large datasets.
Use Case: Researchers can use this to quickly infer the evolutionary relationships of viral variants or protein families, generate publication-quality tree visualizations, and compute statistical support for branching patterns.

Quick Start

Use the phylogenetics skill to perform a full analysis on the provided sequences.fasta file using default settings.

Frequently Asked Questions about phylogenetics

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

FAQPage Schema

How do I automate multiple sequence alignment and phylogenetic tree inference for viral genomes?▼

Automating phylogenetic tree inference requires linking multiple sequence alignment with maximum likelihood tree building. This skill streamlines that pipeline for viral genomes and microbial sequences, using MAFFT for alignment and IQ-TREE 2 for high-accuracy evolutionary reconstruction.

What is the best way to build a phylogenetic tree from a large protein family dataset?▼

Building a phylogenetic tree from a large protein family dataset is best handled with high-speed approximate inference. This skill utilizes FastTree to efficiently generate evolutionary relationships for large biological datasets when maximum likelihood methods become computationally restrictive.

Do I need to install MAFFT and IQ-TREE 2 to run an end-to-end phylogenetics workflow?▼

Yes, you need to install MAFFT and IQ-TREE 2 to run this end-to-end phylogenetics workflow. Executing the full computational pipeline also requires FastTree, ETE3, and matplotlib to support tree inference, evolutionary analysis, and publication-quality visualization.

How does maximum likelihood tree inference compare to FastTree for molecular clock studies?▼

Maximum likelihood tree inference via IQ-TREE 2 provides high-accuracy branching patterns for molecular clock studies, while FastTree offers high-speed approximate inference. This skill supports both approaches, allowing researchers to balance computational speed and phylogenetic accuracy.

Can I generate publication-quality phylogenetic visualizations using ETE3 and matplotlib?▼

Yes, you can generate publication-quality phylogenetic visualizations using ETE3 and matplotlib. This skill integrates both dependencies to compute statistical support for branching patterns and render visual outputs suitable for evolutionary biology research publications.