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)