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Phylogenetic Network
A phylogenetic network 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, the R-package, phangorn, 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. Many kinds and subclasses of phylogenetic networks have been ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graph (discrete Mathematics)
In discrete mathematics, and more specifically in graph theory, a graph is a structure amounting to a Set (mathematics), set of objects in which some pairs of the objects are in some sense "related". The objects correspond to mathematical abstractions called ''Vertex (graph theory), vertices'' (also called ''nodes'' or ''points'') and each of the related pairs of vertices is called an ''edge'' (also called ''link'' or ''line''). Typically, a graph is depicted in diagrammatic form as a set of dots or circles for the vertices, joined by lines or curves for the edges. Graphs are one of the objects of study in discrete mathematics. The edges may be directed or undirected. For example, if the vertices represent people at a party, and there is an edge between two people if they shake hands, then this graph is undirected because any person ''A'' can shake hands with a person ''B'' only if ''B'' also shakes hands with ''A''. In contrast, if an edge from a person ''A'' to a person ''B'' m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SplitsTree
SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, 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. It uses the NEXUS file format. The splits graph is defined using a special data block (SPLITS block). See also *Phylogenetic tree viewers *Dendroscope Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures. Dendroscope can be used for a variety of analyse ... * MEGAN References External links SplitsTree homepage(New Website for informations about SplitsTree)for the latest version (4.15) and manual (June 201 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quasi-median Networks
The concept of a quasi-median network is a generalization of the concept of a median network that was introduced to represent multistate characters. Note that, unlike median networks, quasi-median networks are not split networks. A quasi-median network is defined as a phylogenetic network, the node set of which is given by the quasi-median closure of the condensed version of M (let M be a multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutio ... of DNA sequences on X) and in which any two nodes are joined by an edge if and only if the sequences associated with the nodes differ in exactly one position. The quasi-median closure is defined as the set of all sequences that can be obtained by repeatedly taking the quasi-median of any three sequences in the set and t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Split Networks
For a given set of taxa like X, and a set of splits S on X, usually together with a non-negative weighting, which may represent character changes distance, or may also have a more abstract interpretation, if the set of splits S is compatible, then it can be represented by an unrooted phylogenetic tree and each edge in the tree corresponds to exactly one of the splits. More generally, S can always be represented by a split network, which is an unrooted phylogenetic network A phylogenetic network 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 hybridi ... with the property that every split s in S is represented by an array of parallel edges in the network. A split network N can be obtained from a number of different types of data: *Split networks from distances *Split networks from trees *Split networks from sequence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bijective
In mathematics, a bijection, also known as a bijective function, one-to-one correspondence, or invertible function, is a function between the elements of two sets, where each element of one set is paired with exactly one element of the other set, and each element of the other set is paired with exactly one element of the first set. There are no unpaired elements. In mathematical terms, a bijective function is a one-to-one (injective) and onto (surjective) mapping of a set ''X'' to a set ''Y''. The term ''one-to-one correspondence'' must not be confused with ''one-to-one function'' (an injective function; see figures). A bijection from the set ''X'' to the set ''Y'' has an inverse function from ''Y'' to ''X''. If ''X'' and ''Y'' are finite sets, then the existence of a bijection means they have the same number of elements. For infinite sets, the picture is more complicated, leading to the concept of cardinal number—a way to distinguish the various sizes of infinite sets. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Taxon
In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and given a particular ranking, especially if and when it is accepted or becomes established. It is very common, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion. If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping. Initial attempts at classifying and ordering organisms (plants and animals) were set forth in Carl Linnaeus's Linnaean taxonomy, system in ''Systema Naturae'', 10th edition (1758), as well as an unpublished work by Bernard de Jussieu, Bernard and Antoine Laurent de Jussieu. The idea of a unit-based system of biological classification was first mad ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microevolution
Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection (natural and artificial), gene flow and genetic drift. This change happens over a relatively short (in evolutionary terms) amount of time compared to the changes termed macroevolution. Population genetics is the branch of biology that provides the mathematical structure for the study of the process of microevolution. Ecological genetics concerns itself with observing microevolution in the wild. Typically, observable instances of evolution are examples of microevolution; for example, bacterial strains that have antibiotic resistance. Microevolution may lead to speciation, which provides the raw material for macroevolution. Difference from macroevolution Macroevolution is guided by sorting of interspecific variation ("species selection"), as opposed to sorting of intraspecific variation in microevolution. Species selecti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Distance Matrix
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. Non-metric distance matrix In general, a distance matrix is a weighted adjacency matrix of some graph. In a network, a directed graph with weights assigned to the arcs, the distance between two nodes of the network can be defined as the minimum of the sums of the weights on the shortest paths joining the two nodes. This distance function, while well defined, is not a metric. There need be no restrictions on the weights other than the need to be able to combine and compare them, so negative weights are used in some appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Split (phylogenetics)
A split in phylogenetics is a bipartition of a set of taxon, taxa, and the smallest unit of information in unrooted phylogenetic trees: each edge of an unrooted phylogenetic tree represents one split, and the tree can be efficiently reconstructed from its set of splits. Moreover, when given several trees, the splits occurring in more than half of these trees give rise to a consensus tree, and the splits occurring in a smaller fraction of the trees generally give rise to a consensus Split Network. See also *SplitsTree SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree impleme ..., a program for inferring phylogenetic (split) networks. References {{reflist Phylogenetics Trees (data structures) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Median Graph
In graph theory, a division of mathematics, a median graph is an undirected graph in which every three vertices ''a'', ''b'', and ''c'' have a unique ''median'': a vertex ''m''(''a'',''b'',''c'') that belongs to shortest paths between each pair of ''a'', ''b'', and ''c''. The concept of median graphs has long been studied, for instance by or (more explicitly) by , but the first paper to call them "median graphs" appears to be . As Chung, Graham, and Saks write, "median graphs arise naturally in the study of ordered sets and discrete distributive lattices, and have an extensive literature".. In phylogenetics, the Buneman graph representing all maximum parsimony Phylogenetic tree, evolutionary trees is a median graph. Median graphs also arise in social choice theory: if a set of alternatives has the structure of a median graph, it is possible to derive in an unambiguous way a majority preference among them. Additional surveys of median graphs are given by , , and . Examples ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Newick Format
In mathematics, Newick tree format (or Newick notation or New Hampshire tree format) is a way of representing graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F. James Rohlf, and David Swofford, at two meetings in 1986, the second of which was at Newick's restaurant in Dover, New Hampshire, US. The adopted format is a generalization of the format developed by Meacham in 1984 for the first tree-drawing programs in Felsenstein's PHYLIP package. Examples The following tree: could be represented in Newick format in several ways ((,)); ''no nodes are named'' (A,B,(C,D)); ''leaf nodes are named'' (A,B,(C,D)E)F; ''all nodes are named'' (:0.1,:0.2,(:0.3,:0.4):0.5); ''all but root node have a distance to parent'' (:0.1,:0.2,(:0.3,:0.4):0.5):0.0; ''all hav ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dendroscope
Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures. Dendroscope can be used for a variety of analyses of molecular data sets but is particularly designed for metagenomics or analyses of uncultured environmental samples. It was developed by Daniel Huson and his colleagues at the University of Tübingen in Germany, who also created SplitsTree. See also *List of phylogenetic tree visualization software *SplitsTree *MEGAN Megan is a Welsh feminine given name, originally a diminutive form of Margaret. Margaret is from the Greek μαργαρίτης (''margarítēs''), Latin ''margarīta'', "pearl". Megan is one of the most popular Welsh-language names for women in ... References External links Dendroscope homepage hosted at the University of Washington Phylogenetics software {{science-software-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
