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 Show more