Phylogenetics is a field of biology that studies the evolutionary relationships among various biological species or entities based on their physical and genetic characteristics. This discipline primarily uses the concept of a phylogenetic tree, a diagram that represents the evolutionary pathways and relationships among different organisms, showing how they diverged from common ancestors over time.
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Phylogenetics infers evolutionary relationships from evidence such as anatomy and DNA sequences. A phylogenetic tree summarizes a proposed pattern of ancestry; phylogenetic characters supply the observations, and an inference procedure states how alternative trees are compared.
For sequence data, a nucleotide substitution model assigns probabilities to changes along branches. The phylogenetic pruning algorithm efficiently sums over unknown ancestral states to compute a likelihood function. This connects a historical hypothesis to an explicit calculation rather than treating the most visually similar species as automatically closest relatives.[ref]
Evolutionary trees from DNA sequences: a maximum likelihood approach by Joseph Felsenstein. Ancestral-state summation and likelihood recursion
