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RamanEbrahimi
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phylogenetics

Automate sequence alignment, maximum likelihood tree inference, and tree visualization with MAFFT, IQ-TREE 2, FastTree, and ETE3.

3|Updated Apr 17, 2026
Search Tags:#phylogenetics#evolutionary analysis#sequence alignment#tree inference#maximum likelihood
One-click install
npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill phylogenetics-ramanebrahimi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/RamanEbrahimi/raman-marketplace/tree/main/plugins/agentic-research/skills/scientific-skills/phylogenetics
Command: npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill phylogenetics-ramanebrahimi

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill streamlines the process of building and analyzing phylogenetic trees, automating the alignment, tree inference, and visualization of evolutionary relationships among sequences.

Core Features & Use Cases

  • Multiple Sequence Alignment: Align sequences with MAFFT, ensuring accuracy for small and large datasets.
  • Maximum Likelihood Tree Inference: Build maximum likelihood trees with IQ-TREE 2, handling a variety of sequence types.
  • Fast Approximate ML Tree Inference: Build fast approximate ML trees with FastTree for large datasets.
  • Tree Visualization: Visualize trees with ETE3 or FigTree, aiding in the interpretation of evolutionary history.
  • Use Case: If you have a set of DNA sequences and you want to determine their evolutionary relationships, this Skill can automatically align them, build a maximum likelihood tree, and visualize it.

Quick Start

Run the phylogenetic analysis on the provided DNA sequences with the phylogenetics skill.

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 DNA sequences?▼

To automate multiple sequence alignment and maximum likelihood tree inference for DNA sequences, you can use this Skill to run MAFFT for alignment and IQ-TREE 2 for tree building. It handles the workflow end-to-end, finishing with tree visualization using ETE3.

What is the best way to build a maximum likelihood phylogenetic tree for a large dataset?▼

For building a maximum likelihood phylogenetic tree with a large dataset, the best approach is using FastTree for fast approximate ML tree inference. This Skill integrates FastTree to handle large datasets efficiently where standard ML methods might be too slow.

Do I need to install MAFFT and IQ-TREE 2 before running phylogenetic analysis?▼

Yes, you must install MAFFT, IQ-TREE 2, FastTree, and ETE3 locally before executing this Skill. These external dependencies are required for the multiple sequence alignment, tree inference, and visualization processes to run successfully.

How does maximum likelihood tree inference work for evolutionary analysis?▼

Maximum likelihood tree inference for evolutionary analysis works by evaluating sequence alignment data to find the tree topology with the highest probability of observed mutations. This Skill uses IQ-TREE 2 to calculate these probabilities and visualize evolutionary relationships.

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