query: instance_of splitstree
supports: In mathematics graph theory is the study of "graphs", which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of "vertices", "nodes", or "points" which are connected by "edges", "arcs", or "lines". A graph may be "undirected", meaning that there is no distinction between the two vertices associated with each edge, or its edges may be "directed" from one vertex to another; see Graph (discrete mathematics) for more detailed definitions and for other variations in the types of graph that are commonly considered. Graphs are one of the prime objects of study in discrete mathematics. Deoxyribonucleic acid (DNA) is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids; alongside proteins, lipids and complex carbohydrates (polysaccharides), they are one of the four major types of macromolecules that are essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. In mathematics, a square matrix is a matrix with the same number of rows and columns. An "n"-by-"n" matrix is known as a square matrix of order "n". Any two square matrices of the same order can be added and multiplied.  Evolution is change in the heritable characteristics of biological populations over successive generations. Evolutionary processes give rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms, and molecules. In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the "distance" being used to define this matrix may or may not be a metric. If there are elements, this matrix will have size . In graph-theoretic applications the elements are more often referred to as points, nodes or vertices. Computer science is the study of the theory, experimentation, and engineering that form the basis for the design and use of computers. It is the scientific and practical approach to computation and its applications and the systematic study of the feasibility, structure, expression, and mechanization of the methodical procedures (or algorithms) that underlie the acquisition, representation, processing, storage, communication of, and access to information. An alternate, more succinct definition of computer science is the study of automating algorithmic processes that scale. A computer scientist specializes in the theory of computation and the design of computational systems. Proteins (or ) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity. Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA (mRNA) to convey genetic information (using the letters G, U, A, and C to denote the nitrogenous bases guanine, uracil, adenine, and cytosine) that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome. Nucleotides are organic molecules that serve as the monomers, or subunits, of nucleic acids like DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). The building blocks of nucleic acids, nucleotides are composed of a nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group. A nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a phosphate group yields a nucleotide. Nucleotides are also known as phosphate nucleotides. Amino acids are biologically important organic compounds containing amine (-NH) and carboxyl (-COOH) functional groups, along with a side-chain (R group) specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (-), beta- (-), gamma- (-) or delta- (-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis. In neuropsychology, linguistics and the philosophy of language, a natural language or ordinary language is any language that has evolved naturally in humans through use and repetition without conscious planning or premeditation. Natural languages can take different forms, such as speech, signing, or writing. They are distinguished from constructed and formal languages such as those used to program computers or to study logic. In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
  Sequence alignments are also used for non-biological sequences, such as calculating the edit distance cost between strings in a natural language or in financial data. SplitsTree is a popular program for inferring phylogenetic trees or , more generally , phylogenetic networks from various types of data such as a sequence alignment , a distance matrix or a set of trees . SplitsTree implements published methods such as split decomposition neighbor - net , consensus networks , super networks methods or methods for computing hybridization or simple recombination networks . Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics has been used for "in silico" analyses of biological queries using mathematical and statistical techniques. Mathematics (from Greek  "máthma", knowledge, study, learning) is the study of topics such as quantity (numbers), structure, space, and change. There is a range of views among mathematicians and philosophers as to the exact scope and definition of mathematics. A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly-linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent). Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
candidates: acid activity amine amino acid chain change code complex computer data distance dna field five four graph graph theory group human humans language location mathematics matrix may molecule natural language neurotransmitter number order philosophy quantity reproduction science sequence set side single software space species speech square square matrix structure study theory three will
answer: software