A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), usually an imputed sequence that is not represented in the input. Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. Types of phylogenetic trees and networks The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Maximum Likelihood (also likelihood) optimality criterion is the process of finding the tree topology along with its branch lengths that provides the highest probability observing the sequence data, while parsimony optimality criterion is the fewest number of state-evolutionary changes required for a phylogenetic tree to explain the sequence data. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. Maximum likelihood, parsimony, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Application of computational algorithms, methods and programs to phylogenetic analysesĬomputational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses.
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