# Phylogenetics Tree Builder

> Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships

- Skill: `a5c-ai/phylogenetics-tree-builder` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/phylogenetics-tree-builder`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/phylogenetics-tree-builder/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/phylogenetics-tree-builder

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# Phylogenetics Tree Builder Skill

## Purpose
Enable phylogenetic analysis for constructing evolutionary trees, performing multiple sequence alignments, and assessing phylogenetic relationships.

## Capabilities
- Multiple sequence alignment (MUSCLE, MAFFT)
- Maximum likelihood tree construction
- Bayesian phylogenetic inference
- Bootstrap support calculation
- Tree visualization and annotation
- Molecular clock analysis

## Usage Guidelines
- Align sequences before tree construction
- Select appropriate substitution models
- Calculate bootstrap support for branch confidence
- Visualize trees with meaningful annotations
- Consider molecular clock constraints when appropriate
- Document methodology and parameters

## Dependencies
- RAxML-NG
- IQ-TREE
- MrBayes
- MAFFT
- MUSCLE
- FigTree

## Process Integration
- 16S rRNA Microbiome Analysis (16s-microbiome-analysis)
- Shotgun Metagenomics Pipeline (shotgun-metagenomics)
- Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)