Editing Phylogenetics (section)

== Inference of a phylogenetic tree ==
{{main|Computational phylogenetics}}

Usual methods of [[phylogenetic inference]] involve computational approaches implementing an [[Optimality criterion|optimality criterion]] and methods of [[Maximum parsimony (phylogenetics)|parsimony]], [[maximum likelihood]] (ML), and [[Markov chain Monte Carlo|MCMC]]-based [[Bayesian inference]]. All these depend upon an implicit or explicit [[mathematical model]] describing the relative probabilities of character state transformation within and among the characters observed.<ref>{{Cite book |title=Phylogenetic Inference |url=https://plato.stanford.edu/entries/phylogenetic-inference/ |website=Stanford Encyclopedia of Philosophy|date=15 February 2024 |publisher=Metaphysics Research Lab, Stanford University }}</ref>

[[Phenetics]], popular in the mid-20th century but now largely obsolete, used [[distance matrix]]-based methods to construct trees based on overall similarity in [[morphology (biology)|morphology]] or similar observable traits, which was often assumed to approximate phylogenetic relationships.  [[Neighbor joining|Neighbor Joining]] is a phenetic method that is often used for building similarity trees for [[DNA barcoding|DNA barcodes]].

Prior to 1950, phylogenetic inferences were generally presented as [[narrative]] scenarios. Such methods were often ambiguous and lacked explicit criteria for evaluating alternative hypotheses.<ref>Richard C. Brusca & Gary J. Brusca (2003). ''Invertebrates'' (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. {{ISBN|978-0-87893-097-5}}.</ref><ref>Bock, W. J. (2004). Explanations in systematics. Pp. 49–56. In Williams, D. M. and Forey, P. L. (eds) Milestones in Systematics. London: Systematics Association Special Volume Series 67. CRC Press, Boca Raton, Florida.</ref><ref>Auyang, Sunny Y. (1998). ''Narratives and Theories in Natural History.'' In: ''Foundations of complex-system theories: in economics, evolutionary biology, and statistical physics.'' Cambridge, U.K.; New York: Cambridge University Press.{{page needed|date=June 2018}}</ref>