Bayesian inference in phylogeny

Bayesian inference in phylogeny generates a posterior distribution for a parameter (composed of a phylogenetic tree (its branch lengths and topology) and a model of evolution) based on the prior for that parameter and the likelihood of the data (generated by a multiple alignment). The Bayesian approach has become more popular due to advances in computational machinery, especially, Markov Chain Monte Carlo algorithms. Bayesian inference has a number of applications in molecular phylogenetics, for example, estimation of species phylogeny and species divergence times.

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v t e Phylogenetics
Relevant fields	Computational phylogenetics Molecular phylogenetics Cladistics Taxonomy Evolutionary taxonomy Systematics	Evolutionary biology portal
Basic concepts	Phylogenesis Cladogenesis Phylogenetic tree Cladogram Phylogenetic network Long branch attraction Clade vs Grade Lineage Ghost lineage Ghost population
Inference methods	Maximum parsimony Phylogenetic reconciliation Probabilistic methods Maximum likelihood Bayesian inference Distance-matrix methods Neighbor-joining UPGMA Least squares Three-taxon analysis
Current topics	PhyloCode DNA barcoding Molecular phylogenetics Phylogenetic comparative methods Phylogenetic niche conservatism Phylogenetic signal Phylogenetics software Phylogenomics Phylogeography
Group traits	Primitive Plesiomorphy Symplesiomorphy Derived Apomorphy Synapomorphy Autapomorphy
Group types	Monophyly Paraphyly Polyphyly
Nomenclature	Phylogenetic nomenclature Crown group Sister group Basal Supertree
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