What alignment tools does this skill support?

This skill primarily uses MAFFT, offering various methods like L-INS-i for high accuracy or FFT-NS-i for speed, depending on the dataset size.

Can I build trees for very large datasets?

Yes, the skill includes implementation patterns for FastTree, which is optimized for building approximate maximum likelihood trees for thousands of sequences.

How are the evolutionary trees visualized?

The skill utilizes the ETE3 library to render trees into images (PNG/PDF), supporting both rectangular and circular layouts with customizable node styling.

Does it support both DNA and Protein sequences?

Absolutely. It includes model selection guides for both nucleotide (DNA) and amino acid (protein) data, ensuring the correct evolutionary models are applied.

Phylogenetics & Evolutionary Analysis

Name: Phylogenetics & Evolutionary Analysis
Author: Yezez9

byYezez9

0•

データサイエンスとML

Builds and analyzes phylogenetic trees to infer evolutionary relationships between biological sequences using industry-standard bioinformatics tools.

This skill provides a comprehensive toolkit for performing phylogenetic workflows within Claude Code, covering everything from sequence alignment to tree visualization. It integrates powerful command-line tools like MAFFT for alignment, IQ-TREE 2 for maximum likelihood inference, and FastTree for large-scale datasets. Whether you are tracing viral outbreaks, studying protein family evolution, or detecting horizontal gene transfer, this skill offers the domain-specific guidance and implementation patterns needed to generate high-quality evolutionary insights and publication-ready tree visualizations.

主な機能

01Multiple sequence alignment with MAFFT supporting auto-selection and high-accuracy modes.

02Maximum likelihood tree inference using IQ-TREE 2 with automated model selection.

03Fast approximate ML tree building via FastTree for datasets exceeding 1,000 sequences.

040 GitHub stars

05Publication-quality tree manipulation and visualization using the ETE3 Python library.

06Automated end-to-end pipeline scripts for sequence-to-tree analysis.

ユースケース

01Protein family analysis to infer relationships and conduct ancestral sequence reconstruction.

02Microbial genomics for species phylogeny using 16S rRNA or core genome data.

03Viral phylodynamics to trace outbreak transmission and estimate divergence dates.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent phylogenetics

For use in Claude.ai and ChatGPT

主な機能

01Multiple sequence alignment with MAFFT supporting auto-selection and high-accuracy modes.

02Maximum likelihood tree inference using IQ-TREE 2 with automated model selection.

03Fast approximate ML tree building via FastTree for datasets exceeding 1,000 sequences.

040 GitHub stars

05Publication-quality tree manipulation and visualization using the ETE3 Python library.

06Automated end-to-end pipeline scripts for sequence-to-tree analysis.

ユースケース

01Protein family analysis to infer relationships and conduct ancestral sequence reconstruction.

02Microbial genomics for species phylogeny using 16S rRNA or core genome data.

03Viral phylodynamics to trace outbreak transmission and estimate divergence dates.