---

name: phylogenetics-tree-builder description: Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • sequence-analysis
  • phylogenetics
  • evolution
  • trees graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:graph-algorithms, skill-area:statistical-analysis, skill-area:mathematical-reasoning] workflows: [workflow:experiment-design] roles: [role:research-scientist, role:computational-scientist]

---

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)