Concepts inAlgorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor.
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Cladistics
Cladistics is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants (and nothing else). For example, birds, dinosaurs, crocodiles, and all descendants (living or extinct) of their most recent common ancestor form a clade. In the terms of biological systematics, a clade is a single "branch" on the "tree of life", a monophyletic group.
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Perfect phylogeny
Perfect phylogeny is a term used in computational phylogenetics to denote a phylogenetic tree in which all internal nodes may be labeled as such that all characters evolve down the tree without homoplasy. That is, characteristics do not hold to evolutionary convergence, and do not have analogous structures.
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Phylogenetics
In biology, phylogenetics is the study of evolutionary relation among groups of organisms, which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics derives from the Greek terms phyle (¿¿¿¿) and phylon (¿¿¿¿¿), denoting "tribe" and "race"; and the term genetikos (¿¿¿¿¿¿¿¿¿), denoting "relative to birth", from genesis (¿¿¿¿¿¿¿) "origin" and "birth".
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Parameterized complexity
In computer science, parameterized complexity is a branch of computational complexity theory that focuses on classifying computational problems according to their inherent difficulty with respect to multiple parameters of the input. The complexity of a problem is then measured as a function in those parameters. This allows to classify NP-hard problems on a finer scale than in the classical setting, where the complexity of a problem is only measured by the number of bits in the input.
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Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. These random sequences can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. They can also be induced by the organism itself, by cellular processes such as hypermutation.
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