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phylogenetic-methods

Build and compare phylogenetic trees from sequence alignments using distance-based, maximum-likelihood, and Bayesian methods.

Updated Nov 20, 2025
Search Tags:#alignment#bootstrap#ML#phylogenetics#tree-building#UPGMA#NJ
One-click install
npx skills add https://github.com/roeimed0/rrna-phylo --skill phylogenetic-methods
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phylogenetic-methods
Source: https://github.com/roeimed0/rrna-phylo/tree/main/.claude/skills/phylogenetic-methods
Command: npx skills add https://github.com/roeimed0/rrna-phylo --skill phylogenetic-methods

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Researchers often struggle to construct and evaluate phylogenetic trees from sequence data, juggling multiple methods, alignment requirements, and inconsistent outputs. This Skill provides a cohesive framework to implement and compare distance-based, ML, and Bayesian approaches in a reproducible manner.

Core Features & Use Cases

  • Distance-based methods (UPGMA, Neighbor-Joining) for rapid exploratory trees from distance matrices.
  • Maximum Likelihood & Bayesian methods (e.g., RAxML-NG, IQ-TREE, MrBayes, BEAST) for rigorous inference with model selection and support assessments.
  • Alignment, distance matrices, and formats: support for generating alignments, calculating distances, and exporting trees in Newick/Nexus formats.
  • Bootstrap and support evaluation: tools to perform resampling and map support values onto trees.
  • Comparison & visualization: utilities to compare topologies and visualize trees for interpretation.
  • Real-world use case: Given a multiple sequence alignment, build multiple trees with different methods, compare bootstrap supports, and present a consensus.

Quick Start

Start by preparing a sequence alignment, choose a method (e.g., UPGMA for quick view, ML for publication-quality trees), run distance calculation, build trees, and compare them. Use helper utilities to export results to Newick or Nexus formats.

Frequently Asked Questions about phylogenetic-methods

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I build a phylogenetic tree from a sequence alignment?▼

To build a phylogenetic tree from a sequence alignment, choose distance-based methods like UPGMA for rapid exploratory trees or maximum-likelihood approaches like RAxML-NG and IQ-TREE for publication-quality inferences. The workflow involves calculating distances, building trees, and exporting results to Newick or Nexus formats.

What is the difference between UPGMA and Neighbor-Joining for tree building?▼

UPGMA and Neighbor-Joining are both distance-based methods for building phylogenetic trees from distance matrices. The Skill supports both UPGMA and Neighbor-Joining specifically for generating rapid exploratory trees before committing to more computationally intensive maximum-likelihood or Bayesian inference methods.

Do I need Biopython and ete3 to run phylogenetic tree analysis?▼

Yes, you need external software and libraries such as Biopython, ete3, RAxML-NG, IQ-TREE, and MrBayes to perform phylogenetic tree analysis. These dependencies are required for executing alignment, model selection, bootstrapping, and tree format conversions within the Skill's workflow.

How do I perform bootstrap resampling and map support values onto a phylogenetic tree?▼

To perform bootstrap resampling and map support values onto a phylogenetic tree, the Skill provides dedicated tools to perform resampling and evaluate support assessments. This allows you to compare bootstrap supports between trees built with different methods and present a consensus topology.

Can I use MrBayes and BEAST for Bayesian phylogenetic inference?▼

Yes, you can use MrBayes and BEAST for Bayesian phylogenetic inference. The Skill supports these Bayesian methods alongside maximum-likelihood tools like RAxML-NG and IQ-TREE, enabling rigorous inference with model selection and support assessments for publication-quality results.

What is the best way to compare tree topologies and export to Newick or Nexus formats?▼

The best way to compare tree topologies and export to Newick or Nexus formats is using the Skill's built-in comparison and visualization utilities. These helper utilities allow you to compare topologies built with different methods, interpret results visually, and export trees in standard Newick or Nexus formats.

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