phylogenetics
Phylogenetics
Overview
Phylogenetic analysis reconstructs the evolutionary history of biological sequences (genes, proteins, genomes) by inferring the branching pattern of descent. This skill covers the standard pipeline:
- MAFFT — Multiple sequence alignment
- IQ-TREE 2 — Maximum likelihood tree inference with model selection
- FastTree — Fast approximate maximum likelihood (for large datasets)
- ETE3 — Python library for tree manipulation and visualization
Installation:
# Conda (recommended for CLI tools)
conda install -c bioconda mafft iqtree fasttree
pip install ete3
When to Use This Skill
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