phylogenetics

Builds and analyzes phylogenetic trees from sequence data using MAFFT, IQ-TREE 2, and ETE3.

22|4|Updated May 25, 2026

Search Tags:#bioinformatics #phylogenetics #tree-inference #sequence-alignment #evolutionary-analysis #ETE3

Ready to run

npx skills add https://github.com/crazymsn/academic-skills --skill phylogenetics-crazymsn

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/crazymsn/academic-skills/tree/main/academic-skills/phylogenetics
Command: npx skills add https://github.com/crazymsn/academic-skills --skill phylogenetics-crazymsn

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Phylogenetic analysis helps researchers reconstruct evolutionary histories from sequence data, enabling insights into relationships, timings, and functional evolution.

Core Features & Use Cases

Multiple Sequence Alignment with MAFFT
Maximum Likelihood tree inference using IQ-TREE 2, with FastTree for large datasets
Tree visualization with ETE3 or FigTree
Outgroup rooting and bootstrap-supported phylogenies
Molecular clock dating and comparative genomics

Quick Start

Run the pipeline on your unaligned FASTA file to generate a final phylogenetic tree and visualizations.

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 unaligned FASTA sequences?▼

You build a phylogenetic tree by running a standard pipeline that performs multiple sequence alignment with MAFFT, infers the tree using IQ-TREE 2, and visualizes the results with ETE3.

What is the best way to infer evolutionary relationships for large genomic datasets?▼

For large genomic datasets, phylogenetic analysis can use FastTree for efficient tree inference instead of IQ-TREE 2, while still supporting bootstrap values to ensure evolutionary relationship accuracy.

Can I use MAFFT and IQ-TREE 2 for viral phylodynamics and outbreak tracing?▼

Yes, MAFFT and IQ-TREE 2 can be used for viral phylodynamics and outbreak tracing by reconstructing evolutionary histories from viral sequence data to track relationships and timings.

Does this phylogenetic analysis pipeline support outgroup rooting and bootstrap support?▼

Yes, the phylogenetic analysis pipeline supports optional outgroup rooting and bootstrap-supported phylogenies to establish correct tree topology and assess evolutionary relationship confidence.

How do I visualize a phylogenetic tree after maximum likelihood inference?▼

To visualize a phylogenetic tree after maximum likelihood inference, use ETE3 or FigTree to render the final topology and analyze the evolutionary relationships directly.