Phylogenetics

Reconstruction of evolutionary trees from sequence data: substitution models, likelihood and parsimony, distance methods, tree metrics, splits and the enumeration of phylogenetic trees.

• Counting binary phylogenetic trees
• Felsenstein's pruning algorithm
• Jukes–Cantor model
• Maximum-likelihood ancestral reconstruction
• Neighbor joining
• Atteson's theorem on neighbor joining
• Neighbor joining and balanced minimum evolution
• Pauplin's formula and balanced minimum evolution
• PhyloCSF coding classifier
• Small parsimony problem
• Pulley principle, LogDet distances and Felsenstein zone
• Time-reversible nucleotide substitution models
• Codon substitution models and dN/dS
• Tree metrics and the four-point condition
• Splits, compatibility, ultrametrics and UPGMA
• Evolutionary conservation scores

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