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phylogenetics

Aligns biological sequences with MAFFT and infers evolutionary trees via IQ-TREE 2 or FastTree.

1|Updated Mar 12, 2026
Search Tags:#bioinformatics#genomics#phylogenetics#evolutionary analysis#sequence alignment#tree inference
One-click install
npx skills add https://github.com/yf8578/clawomics --skill phylogenetics-yf8578
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/yf8578/clawomics/tree/main/skills/phylogenetics
Command: npx skills add https://github.com/yf8578/clawomics --skill phylogenetics-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires mafft, iqtree2, ete3, 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, turning raw genetic or protein data into interpretable phylogenetic trees.

Core Features & Use Cases

  • Multiple Sequence Alignment: Uses MAFFT for accurate sequence alignment.
  • Phylogenetic Tree Inference: Builds trees using IQ-TREE 2 (maximum likelihood) or FastTree (fast approximate ML).
  • Visualization: Generates tree visualizations using ETE3.
  • Use Case: Analyze the evolutionary divergence of a set of viral genomes to understand outbreak patterns or classify newly discovered microbial species based on their genetic relatedness.

Quick Start

Run a full phylogenetic analysis on the provided DNA sequences in 'sequences.fasta'.

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 raw DNA sequences?▼

To build a phylogenetic tree from raw DNA sequences, this Skill performs multiple sequence alignment using MAFFT, followed by maximum likelihood tree inference using IQ-TREE 2, and finally visualizes the evolutionary relationships with ETE3.

What is the best way to infer evolutionary relationships for viral genomes?▼

The best way to infer evolutionary relationships for viral genomes is using maximum likelihood phylogenetic analysis, which aligns genomic sequences with MAFFT and constructs accurate evolutionary trees using IQ-TREE 2 to understand outbreak patterns and genetic divergence.

Does this phylogenetic analysis workflow support amino acid sequences?▼

Yes, this phylogenetic analysis workflow supports both nucleotide and amino acid sequences, allowing you to align biological sequences with MAFFT and infer molecular evolution trees using IQ-TREE 2 or FastTree for evolutionary biology studies.

Can I use FastTree instead of IQ-TREE 2 for tree inference?▼

Yes, you can use FastTree for fast approximate maximum likelihood tree inference as an alternative to IQ-TREE 2, providing a faster route to infer evolutionary trees when analyzing biological sequences for genomics studies.

Do I need to install MAFFT and ETE3 to run this sequence alignment workflow?▼

Yes, you must install MAFFT, IQ-TREE 2, and ETE3 in your environment to execute this sequence alignment workflow, as these dependencies are required for accurate alignment, tree inference, and tree visualization.

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