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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, and are represented using a type of phylogenetic network called a 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/Phangorn packages. Examples of the application of Neighbor-net can be found in virology, horticulture, dinosaur genetics, comparative linguistics Comparative linguistics is a branch of historical linguistics that is concerned with comparing languages to establish their historical relatedness. Genetic relatedness implies a common origin or proto-language and comparative ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SplitsTree
SplitsTree is a freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, split graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. Software SplitsTree implements published methods such as split (phylogenetics), split decomposition, neighbor-net, consensus networks, super networks methods or methods for computing Hybrid (biology), hybridization or simple genetic recombination, recombination networks. It uses the Nexus file, NEXUS file format. The splits graph is defined using a special data block (SPLITS block). See also *Phylogenetic tree viewers *Dendroscope *MEGAN References {{Reflist External links SplitsTree homepage(New Website for informations about SplitsTree)for the latest version (4.15) and manual (June 2019), hosted by thDepartment of Computer Scienceat the University of Tübingen, Eberhard Karls University TübingenAlgorithms in Bioinformatics Daniel Huson's working group deve ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heterobranchia Tree
Heterobranchia, the heterobranchs (meaning "different gill"), is a taxonomic clade of snails and slugs, which includes marine, aquatic, and terrestrial gastropod molluscs. Heterobranchia is one of the main clades of gastropods. Currently Heterobranchia comprises two groups: the opisthobranchs, and the pulmonates. Diversity The two subdivisions of this large clade are quite diverse: * Opisthobranchia are virtually all marine species, some shelled and some not, and comprise about 25 families and 2000 species of the bubble shells, the seaslugs, as well as the sea hares. The internal organs of the opisthobranchs have undergone detorsion (unwinding of the viscera that were twisted during torsion). * The Pulmonata comprises about 20000 species, includes the majority of land snails and slugs, many freshwater snails, and a small number of marine species. The mantle cavity of the Pulmonata is modified into an air-breathing organ. They are also characterized by detorsion and a ... [...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 bee ... [...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 (mathematics), 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 (mathematics), 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 (where the number of steps in the path is bounded). This distance function, while well defined, is not a metric. There need be no restrictions on the weights oth ... [...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 = (n' ... [...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 , where they called these graphs "polar graphs" (). 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 a ... [...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 In the theory of computational complexity, the travelling salesman problem (TSP) asks the following question: "Given a list of cities and the distances between each pair of cities, what is the shortest possible route that visits each city exac .... These conditions apply to a special kind of cost matrix, the Kalmanson matrix, and are named after Kenneth Kalmanson. References *. *. *. *. *. Combinatorics {{combin-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
R (programming Language)
R is a programming language for statistical computing and Data and information visualization, data visualization. It has been widely adopted in the fields of data mining, bioinformatics, data analysis, and data science. The core R language is extended by a large number of R package, software packages, which contain Reusability, reusable code, documentation, and sample data. Some of the most popular R packages are in the tidyverse collection, which enhances functionality for visualizing, transforming, and modelling data, as well as improves the ease of programming (according to the authors and users). R is free and open-source software distributed under the GNU General Public License. The language is implemented primarily in C (programming language), C, Fortran, and Self-hosting (compilers), R itself. Preprocessor, Precompiled executables are available for the major operating systems (including Linux, MacOS, and Microsoft Windows). Its core is an interpreted language with a na ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantitative Comparative Linguistics
Quantitative comparative linguistics is the use of quantitative research, 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, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Phylogenetics
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, Heuristic (computer science), heuristics, and approaches involved in Phylogenetics, phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood estimation, Maximum likelihood, Maximum parsimony (phylogenetics), parsimony, Bayesian inference in phylogeny, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space. Maximum Likelihood (al ... [...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 conte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
