Agent-Skills.md

Agent Skills: Phylogenetics Tree Builder Skill

Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships

bioinformaticsID: a5c-ai/babysitter/phylogenetics-tree-builder

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/phylogenetics-tree-builder

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/phylogenetics-tree-builder/SKILL.md

Skill Metadata

Name
phylogenetics-tree-builder
Description
Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships

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)