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Phylogenetics tree builder

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/phylogenetics-tree-builder

Phylogenetic analysis skill for constructing evolutionary trees and assessing relationshipsFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill phylogenetics-tree-builder

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.7 KB, 209 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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