phylogenetics-tree-builder

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)