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bio-phylogenetics

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

Updated Mar 13, 2026
Search Tags:#bioinformatics#genomics#phylogenetics#sequence alignment#iqtree#mafft#evolutionary tree
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill bio-phylogenetics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-phylogenetics
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/bio-phylogenetics
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill bio-phylogenetics

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the complex process of reconstructing evolutionary relationships between biological sequences, enabling deep insights into evolution, disease spread, and genetic diversity.

Core Features & Use Cases

  • Automated Phylogeny Pipeline: Integrates alignment (MAFFT), tree inference (IQ-TREE 2, FastTree), and visualization (ETE3).
  • Versatile Applications: Ideal for evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
  • Use Case: Analyze the evolutionary relationships of a set of newly discovered viral sequences to understand their origin and spread during an outbreak.

Quick Start

Run a full phylogenetic analysis on the provided nucleotide sequences in 'sequences.fasta' using 8 threads.

Frequently Asked Questions about bio-phylogenetics

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

FAQPage Schema
How do I build a phylogenetic tree from multiple sequence alignments?▼

This Skill builds a phylogenetic tree by running an automated pipeline: MAFFT performs multiple sequence alignment, IQ-TREE 2 or FastTree infers the tree, and ETE3 visualizes the evolutionary relationships.

Can I use IQ-TREE 2 for viral phylodynamics and outbreak sequence analysis?▼

Yes, IQ-TREE 2 is integrated for maximum likelihood inference, making it suitable for viral phylodynamics and analyzing the evolutionary relationships of newly discovered viral sequences during an outbreak.

What is the best way to visualize an evolutionary tree generated from genomics data?▼

The best way to visualize an evolutionary tree from genomics data here is using ETE3, which is integrated into the pipeline to render and analyze the phylogenetic trees inferred by IQ-TREE 2 or FastTree.

Does this phylogenetics pipeline support both nucleotide and protein family analysis?▼

Yes, the phylogenetics pipeline supports protein family analysis and molecular clock studies alongside microbial genomics, applying maximum likelihood inference and multiple sequence alignment to biological sequences.

When should I use FastTree instead of IQ-TREE 2 for evolutionary tree inference?▼

You should use FastTree for approximate maximum likelihood inference when needing faster results, whereas IQ-TREE 2 is utilized for more rigorous maximum likelihood tree inference within the phylogenetic analysis pipeline.

Do I need to run MAFFT separately before inferring a phylogenetic tree?▼

No, you do not need to run MAFFT separately; the pipeline automates the multiple sequence alignment step internally before passing the aligned sequences to IQ-TREE 2 or FastTree for tree inference.

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