phylogenetics

Construct phylogenetic trees from biological sequences using MAFFT, IQ-TREE 2, and FastTree.

Updated May 17, 2026

Search Tags:#sequence analysis #evolutionary biology #phylogenetics #tree inference #molecular clock

Ready to run

npx skills add https://github.com/galeep/plugin-place --skill phylogenetics-galeep

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-bioinformatics-genomics/skills/phylogenetics
Command: npx skills add https://github.com/galeep/plugin-place --skill phylogenetics-galeep

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires mafft, iqtree2, 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, offering a streamlined solution for evolutionary biology research.

Core Features & Use Cases

Phylogenetic Tree Construction: Align sequences, infer tree structures using various methods, and perform model selection.
Tree Visualization: Render trees with detailed statistics and support values.
Use Case: Ideal for evolutionary biologists seeking to reconstruct the evolutionary history of biological sequences and infer relationships between species.

Quick Start

Run the phylogenetic analysis pipeline with the command: python phylogenetic_analysis.py sequences.fasta --type nt --threads 4

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 multiple sequence alignments?▼

You can construct phylogenetic trees from biological sequences by providing a FASTA file to the pipeline. The Skill utilizes MAFFT for sequence alignment and IQ-TREE 2 or FastTree for tree inference and model selection.

What is the best way to visualize phylogenetic trees with statistical support values?▼

Visualizing phylogenetic trees with support values is handled by the ETE3 dependency, which renders detailed tree structures. The Skill provides visualization capabilities to display inferred trees alongside their statistical support values.

Do I need to install MAFFT and IQ-TREE 2 to infer evolutionary relationships?▼

Yes, MAFFT, IQ-TREE 2, FastTree, and ETE3 are required dependencies to infer evolutionary relationships. These tools must be installed in your environment to execute the sequence alignment, tree inference, and visualization processes.

Can I use this pipeline for molecular clock studies and evolutionary biology research?▼

Yes, this Skill is applicable to molecular clock studies and evolutionary biology research. It constructs phylogenetic trees from biological sequences to help reconstruct evolutionary history and infer relationships between species.

Does phylogenetic tree construction support nucleotide and protein sequence analysis?▼

Phylogenetic tree construction supports nucleotide sequence analysis, as specified by the nucleotide type parameter in the pipeline command. It processes standard FASTA biological sequences for alignment and tree inference.