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Genomic distances under deletions and insertions

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Genome

In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome.

Evolutionary biology

Evolutionary biology is the subfield of biology that studies the evolutionary processes (natural selection, common descent, speciation) that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes (physical characteristics) of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed onto their offspring.

Edit distance

In computational linguistics and computer science, edit distance is a string metric, i.e. a way of quantifying how dissimilar two strings (e.g., words) are to one another, that is measured by counting the minimum number of operations required to transform one string into the other. Edit distances find applications in natural language processing, where automatic spelling correction can determine candidate corrections for a misspelled word by selecting words from a dictionary that have a low distance to the word in question.

Polynomial-time reduction

In computational complexity theory, a polynomial-time reduction is a method for solving one problem using another. One shows that if a hypothetical subroutine solving the second problem exists, then the first problem can be solved by transforming or reducing it to inputs for the second problem and calling the subroutine one or more times. If both the time required to transform the first problem to the second, and the number of times the subroutine is called is polynomial, then the first problem is polynomial-time reducible to the second.

Polynomial hierarchy

In computational complexity theory, the polynomial hierarchy (sometimes called the polynomial-time hierarchy) is a hierarchy of complexity classes that generalize the classes NP and co-NP. Each class in the hierarchy is contained within PSPACE. The hierarchy can be defined using oracle machines or alternating Turing machines. It is a resource-bounded counterpart to the arithmetical hierarchy and analytical hierarchy from mathematical logic. The union of the classes in the hierarchy is denoted PH.

Time complexity

In computer science, the time complexity is the computational complexity that describes the amount of computer time it takes to run an algorithm. Time complexity is commonly estimated by counting the number of elementary operations performed by the algorithm, supposing that each elementary operation takes a fixed amount of time to perform. Thus, the amount of time taken and the number of elementary operations performed by the algorithm are taken to be related by a constant factor.

NP (complexity)

In computational complexity theory, NP (nondeterministic polynomial time) is a complexity class used to classify decision problems. NP is the set of decision problems for which the problem instances, where the answer is "yes", have proofs verifiable in polynomial time by a deterministic Turing machine, or alternatively the set of problems that can be solved in polynomial time by a nondeterministic Turing machine. NP is the set of decision problems solvable in polynomial time by a nondeterministic Turing machine.

Parity of a permutation

In mathematics, when X is a finite set with at least two elements, the permutations of X (i.e. the bijective functions from X to X) fall into two classes of equal size: the even permutations and the odd permutations. If any total ordering of X is fixed, the parity (oddness or evenness) of a permutation of X can be defined as the parity of the number of inversions for σ, i.e., of pairs of elements x, y of X such that x < y and σ(x) > σ(y). The sign, signature, or signum of a permutation σ is denoted sgn(σ) and defined as +1 if σ is even and −1 if σ is odd.

History of evolutionary thought

Evolutionary thought, the recognition that species change over time and the perceived understanding of how such processes work, has roots in antiquity—in the ideas of the ancient Greeks, Romans, Chinese, Church Fathers as well as in medieval Islamic science.

Polynomial-time approximation scheme

In computer science (particularly algorithmics), a polynomial-time approximation scheme (PTAS) is a type of approximation algorithm for optimization problems (most often, NP-hard optimization problems). A PTAS is an algorithm which takes an instance of an optimization problem and a parameter ε > 0 and produces a solution that is within a factor 1 + ε of being optimal (or 1 – ε for maximization problems). For example, for the Euclidean traveling salesman problem, a PTAS would produce a tour with length at most (1 + ε)L, with L being the length of the shortest tour.