phylogenetics

Name: phylogenetics
Availability: InStock
Author: K-Dense

Align sequences with MAFFT, infer maximum-likelihood trees with IQ-TREE 2, and visualize results.

33.0k|3.2k|Updated Oct 19, 2025

Search Tags:#alignment #phylogeny #ete3 #phylogenetics #iq-tree #tree-visualization #mafft

Ready to run

npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill phylogenetics-k-dense-ai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: phylogenetics
Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/phylogenetics
Command: npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill phylogenetics-k-dense-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

Phylogenetic analysis reconstructs evolutionary relationships from biological sequences and provides an integrated workflow to produce reliable trees, alignments, and visualizations.

Core Features & Use Cases

Multiple Sequence Alignment with MAFFT
Maximum Likelihood Tree Inference with IQ-TREE 2 (model selection)
FastTree alternative for large datasets
Visualization with ETE3 or FigTree
Use cases: viral phylodynamics, microbial genomics, protein family analysis, molecular clock studies

Quick Start

Provide an unaligned FASTA file; the pipeline will align sequences, infer a ML tree, and render a visualization.

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 end-to-end?▼

To build a phylogenetic tree from a FASTA file, the pipeline performs multiple sequence alignment with MAFFT, maximum-likelihood tree inference with IQ-TREE 2, and visualization with ETE3 to render the final phylogenetic results.

When should I use FastTree instead of IQ-TREE 2 for phylogenetic analysis?▼

For phylogenetic analysis, you should use FastTree instead of IQ-TREE 2 when handling large genomic datasets. IQ-TREE 2 performs thorough maximum-likelihood model selection for smaller datasets, while FastTree provides faster inference for large-scale sequence alignments.

What is the best way to visualize a phylogenetic tree for publication?▼

The best way to visualize a phylogenetic tree for publication is using ETE3 or FigTree tree-visualization tools, which render inferred maximum-likelihood phylogenetic trees into graphical outputs suitable for evolutionary studies.

Do I need aligned sequences to infer a maximum-likelihood phylogenetic tree?▼

No, you do not need aligned sequences to infer a phylogenetic tree. You can provide an unaligned FASTA file and the pipeline will perform multiple sequence alignment using MAFFT before inferring the tree with IQ-TREE 2.

Can I use this phylogenetic pipeline for viral phylodynamics and microbial genomics?▼

Yes, you can use this phylogenetic pipeline for viral phylodynamics and microbial genomics. It applies maximum-likelihood phylogenetic analysis to evolutionary studies, handling datasets from small gene families to large genomic datasets.