phylogenetics-tree-builder

Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships

509 stars

Best use case

phylogenetics-tree-builder is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships

Teams using phylogenetics-tree-builder should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

You only need a quick one-off answer and do not need a reusable workflow.
You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/phylogenetics-tree-builder/SKILL.md --create-dirs "https://raw.githubusercontent.com/a5c-ai/babysitter/main/library/specializations/domains/science/bioinformatics/skills/phylogenetics-tree-builder/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/phylogenetics-tree-builder/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How phylogenetics-tree-builder Compares

Feature / Agent	phylogenetics-tree-builder	Standard Approach
Platform Support	Not specified	Limited / Varies
Context Awareness	High	Baseline
Installation Complexity	Unknown	N/A

Frequently Asked Questions

What does this skill do?

Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# 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)

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