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Neighbor-net
NeighborNet is an algorithm for constructing phylogenetic networks which is loosely based on the neighbor joining algorithm. Like neighbor joining, the method takes a distance matrix as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a hierarchy (mathematics), hierarchy, and are represented using a type of phylogenetic network called a Split graph, splits graph. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering. The method is implemented in the SplitsTree and R (programming language), R/Phangorn packages. Examples of the application of Neighbor-net can be found in virology, horticulture, dinosaur genetics, Quantitative comparative linguistics, comparative linguistics, and archaeology. References Computational phylogenetics Genetics software Molecular biology {{bioinformatics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantitative Comparative Linguistics
Quantitative comparative linguistics is the use of quantitative analysis as applied to comparative linguistics. Examples include the statistical fields of lexicostatistics and glottochronology, and the borrowing of phylogenetics from biology. History Statistical methods have been used for the purpose of quantitative analysis in comparative linguistics for more than a century. During the 1950s, the Swadesh list emerged: a standardised set of lexical concepts found in most languages, as words or phrases, that allow two or more languages to be compared and contrasted empirically. Probably the first published quantitative historical linguistics study was by Sapir in 1916, while Kroeber and Chretien in 1937 investigated nine Indo-European (IE) languages using 74 morphological and phonological features (extended in 1939 by the inclusion of Hittite). Ross in 1950 carried out an investigation into the theoretical basis for such studies. Swadesh, using word lists, developed lexicosta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heterobranchia Tree
Heterobranchia, the ''heterobranchs'' (meaning "different-gilled snails"), is a taxonomic clade of snails and slugs, which includes marine, aquatic and terrestrial gastropod mollusks. Heterobranchia is one of the main clades of gastropods. Currently Heterobranchia comprises three informal groups: the lower heterobranchs, the opisthobranchs and the pulmonates.Bouchet P. & Rocroi J.-P. (Ed.); Frýda J., Hausdorf B., Ponder W., Valdes A. & Warén A. 2005. ''Classification and nomenclator of gastropod families''. Malacologia: International Journal of Malacology, 47(1-2). ConchBooks: Hackenheim, Germany. . . 397 pp. http://www.vliz.be/Vmdcdata/imis2/ref.php?refid=78278 Diversity The three subdivisions of this large clade are quite diverse: * The Lower Heterobranchia includes shelled marine and freshwater species. * Opisthobranchia are almost all marine species, some shelled and some not. The internal organs of the opisthobranchs have undergone detorsion (unwinding of the vis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
Neighbor Joining
In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987. Usually based on DNA or protein sequence data, the algorithm requires knowledge of the distance between each pair of taxa (e.g., species or sequences) to create the phylogenetic tree. The algorithm Neighbor joining takes a distance matrix, which specifies the distance between each pair of taxa, as input. The algorithm starts with a completely unresolved tree, whose topology corresponds to that of a star network, and iterates over the following steps, until the tree is completely resolved, and all branch lengths are known: # Based on the current distance matrix, calculate a matrix Q (defined below). # Find the pair of distinct taxa i and j (i.e. with i \neq j) for which Q(i,j) is smallest. Make a new node that joins the taxa i and j, and connect the new node to the central node. For example, in part (B ... [...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] |
Hierarchy (mathematics)
In mathematics, a hierarchy is a set-theoretical object, consisting of a preorder defined on a set. This is often referred to as an ordered set, though that is an ambiguous term that many authors reserve for partially ordered sets or totally ordered sets. The term ''pre-ordered set'' is unambiguous, and is always synonymous with a mathematical hierarchy. The term ''hierarchy'' is used to stress a '' hierarchical'' relation among the elements. Sometimes, a set comes equipped with a natural hierarchical structure. For example, the set of natural numbers N is equipped with a natural pre-order structure, where n \le n' whenever we can find some other number m so that n + m = n'. That is, n' is bigger than n only because we can get to n' from n ''using'' m. This idea can be applied to any commutative monoid. On the other hand, the set of integers Z requires a more sophisticated argument for its hierarchical structure, since we can always solve the equation n + m = n' by writing m = ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Split Graph
In graph theory, a branch of mathematics, a split graph is a graph in which the vertices can be partitioned into a clique and an independent set. Split graphs were first studied by , and independently introduced by . A split graph may have more than one partition into a clique and an independent set; for instance, the path is a split graph, the vertices of which can be partitioned in three different ways: #the clique and the independent set #the clique and the independent set #the clique and the independent set Split graphs can be characterized in terms of their forbidden induced subgraphs: a graph is split if and only if no induced subgraph is a cycle on four or five vertices, or a pair of disjoint edges (the complement of a 4-cycle). Relation to other graph families From the definition, split graphs are clearly closed under complementation. Another characterization of split graphs involves complementation: they are chordal graphs the complements of which are also ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Kalmanson Combinatorial Conditions
In mathematics, the Kalmanson combinatorial conditions are a set of conditions on the distance matrix used in determining the solvability of the traveling salesman problem. These conditions apply to a special kind of cost matrix In production, research, retail, and accounting, a cost is the value of money that has been used up to produce something or deliver a service, and hence is not available for use anymore. In business, the cost may be one of acquisition, in which ..., the Kalmanson matrix, and are named after Kenneth Kalmanson. References *. *. *. *. *. Combinatorics {{combin-stub ... [...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] |
R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Phylogenetics
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic"origin,_source,_birth")_is_the_study_of_the_evolutionary_his_... "origin, source, birth") is the study of the evolutionary his ... "origin, source, birth") is the study of the evolutionary his ... "origin, source, birth") is the study of the evolutionary his ... "origin, source, birth") is the study of the evolutionary his ... "tribe, clan, race", and wikt:γενετικός, γενετικός [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics Software
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance), and within the context ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
