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Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or…
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
don't have the plugin yet? install it then click "run inline in claude" again.