Individual skill
phylogenetics
Molecular phylogenetics — alignment, model selection, tree inference, and interpreting evolutionary trees.
skills/phylogenetics/SKILL.md
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- Last checked
- Nov 11, 2026
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- Oct 10, 2026
- License
- MIT
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## Overview
phylogenetics covers inferring evolutionary relationships from molecular sequences: multiple
sequence alignment, substitution-model selection, tree inference (maximum likelihood,
Bayesian), support assessment, and honest interpretation. Trees are hypotheses with
uncertainty — this skill emphasizes the uncertainty as much as the topology.
## When to use
- Building gene/species trees: marker selection, taxon sampling.
- Alignment: MAFFT/MUSCLE, trimming, alignment QC.
- Model selection: substitution models, partitioning, rate heterogeneity.
- Tree inference: IQ-TREE, RAxML, MrBayes/BEAST — ML vs Bayesian.
- Support: bootstrap, posterior probabilities, and what they mean.