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LeonChaoX
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phylogenetics

Reconstruct phylogenetic trees from FASTA alignments using MAFFT and IQ-TREE 2.

783|65|Updated Feb 27, 2026
Search Tags:#phylogenetics#evolutionary analysis#mafft#fasttree#tree visualization#iq-tree2#bootstrap support
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill phylogenetics-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/05-%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E4%B8%8E%E5%9F%BA%E5%9B%A0%E7%BB%84%E5%AD%A6/phylogenetics
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill phylogenetics-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires subprocess, os, sys, argparse, pathlib, ete3, matplotlib, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps you infer evolutionary relationships from sequence data by building phylogenetic trees and producing interpretable visual outputs.

Core Features & Use Cases

  • Multiple sequence alignment with MAFFT to turn raw FASTA into aligned sequences suitable for tree inference.
  • Maximum-likelihood phylogenetic inference with IQ-TREE 2 (with model selection and ultrafast bootstrap support).
  • Fast alternative with FastTree for large datasets where IQ-TREE is slow, plus tree visualization and inspection with ETE3.
  • Use cases: microbial genomics and species phylogeny, viral phylodynamics, protein family evolution, horizontal gene transfer indications, and molecular clock-focused analyses using dated samples.

Quick Start

Ask the AI to run a complete pipeline that aligns your FASTA with MAFFT, infers an ML tree with IQ-TREE 2 using TEST model selection and 1000 ultrafast bootstraps, roots the tree (midpoint or outgroup), and exports a publication-ready PNG using ETE3.

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 a FASTA file?▼

To build a phylogenetic tree from a FASTA file, you can align sequences with MAFFT, infer a maximum-likelihood tree using IQ-TREE 2 with ultrafast bootstrap, and visualize the rooted tree with ETE3.

What is the best way to run evolutionary analysis on a large dataset?▼

For evolutionary analysis of large datasets where IQ-TREE is slow, FastTree provides a fast alternative to infer phylogenetic trees, while MAFFT handles the initial multiple sequence alignment.

Can I use MAFFT and IQ-TREE 2 for viral phylodynamics and molecular clock workflows?▼

Yes, MAFFT and IQ-TREE 2 support viral phylodynamics and molecular clock workflows by processing dated samples to infer evolutionary relationships and generate trees with bootstrap support.

How do I visualize and root a phylogenetic tree for publication?▼

You can visualize and root a phylogenetic tree for publication using ETE3, which supports midpoint or outgroup rooting and exports interpretable, publication-ready PNG images.

Does this phylogenetic pipeline support protein family evolution and horizontal gene transfer analysis?▼

Yes, this phylogenetic pipeline supports protein family evolution and horizontal gene transfer indications by applying model-based maximum-likelihood inference to aligned protein or nucleotide sequences.

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