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Clustalw
Clustal is a computer program used for multiple sequence alignment in bioinformatics. The software and its algorithms have gone through several iterations, with ClustalΩ (Omega) being the latest version . It is available as standalone software, via a web interface, and through a server hosted by the European Bioinformatics Institute. Clustal has been an important bioinformatic software, with two of its academic publications amongst the top 100 papers cited of all time, according to Nature in 2014. History Version history * Clustal: The original software for multiple sequence alignments, created by Des Higgins in 1988, was based on deriving a guide tree from pairwise sequences of amino acids or nucleotides. * ClustalV: The second generation of Clustal, released in 1992. It introduced the ability to create new alignments from existing alignments in a process known as phylogenetic tree reconstruction. ClustalV also added the option to create trees using the neighbor joini ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Desmond G
Desmond or Desmond's may refer to: Arts and entertainment * ''Desmond'' (novel), 1792 novel by Charlotte Turner Smith * '' Desmond's'', 1990s British television sitcom Ireland * Kingdom of Desmond, medieval Irish kingdom * Earl of Desmond, Irish aristocratic title * Desmond Rebellions, Irish rebellions during the 16th century led by the Earl of Desmond Science and technology * DESMOND (diabetes) (Diabetes Education and Self Management for Ongoing and Newly Diagnosed), a UK NHS diabetes education programme * Desmond (software), molecular dynamics simulation software * Storm Desmond, a windstorm in Britain and Ireland in 2015 Other uses * Desmond (name), a common given name and surname * Desmond (horse) (1896–1913), Thoroughbred racehorse * Desmond's (department store), a former US store * Desmond, slang term for the British 2:2 degree classification * Desmond, Western Australia, a former town in the Shire of Ravensthorpe See also * Desman Desmans are aquatic insectivo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Regina Nuzzo
Regina Nuzzo is a professor of statistics at Gallaudet University in Washington D.C., a liberal arts school for deaf and hard-of-hearing students. She also writes articles about the importance of statistical and science communication and is an advocate for people with disabilities in the science and technology field. Education Nuzzo graduated from the University of South Florida with a Bachelor's degree in industrial engineering and went on to obtain her Ph.D in statistics from Stanford University in 2004, supervised by Richard A. Olshen. Her dissertation was written on the usage of stochastic models in bio-chemistry. Nuzzo also graduated from the University of California Santa Cruz's science writing program, where she learned how to write effectively for a variety of audiences about science and technology. Career Nuzzo has been a faculty member at Gallaudet University since 2006. She has written multiple articles for publication in major magazines, including WIRED magazine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristic
A heuristic or heuristic technique (''problem solving'', '' mental shortcut'', ''rule of thumb'') is any approach to problem solving that employs a pragmatic method that is not fully optimized, perfected, or rationalized, but is nevertheless "good enough" as an approximation or attribute substitution. Where finding an optimal solution is impossible or impractical, heuristic methods can be used to speed up the process of finding a satisfactory solution. Heuristics can be mental shortcuts that ease the cognitive load of making a decision. Context Gigerenzer & Gaissmaier (2011) state that sub-sets of ''strategy'' include heuristics, regression analysis, and Bayesian inference. Heuristics are strategies based on rules to generate optimal decisions, like the anchoring effect and utility maximization problem. These strategies depend on using readily accessible, though loosely applicable, information to control problem solving in human beings, machines and abstract i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X Window System
The X Window System (X11, or simply X) is a windowing system for bitmap displays, common on Unix-like operating systems. X originated as part of Project Athena at Massachusetts Institute of Technology (MIT) in 1984. The X protocol has been at version 11 (hence "X11") since September 1987. The X.Org Foundation leads the X project, with the current reference implementation, X.Org Server, available as free and open-source software under the MIT License and similar permissive licenses. Purpose and abilities X is an architecture-independent system for remote graphical user interfaces and input device capabilities. Each person using a networked computer terminal, terminal has the ability to interact with the display with any type of user input device. In its standard distribution it is a complete, albeit simple, display and interface solution which delivers a standard widget toolkit, toolkit and protocol stack for building graphical user interfaces on most Unix-like operating syst ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UPGMA
UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. It also has a weighted variant, WPGMA, and they are generally attributed to Sokal and Michener. Note that the unweighted term indicates that all distances contribute equally to each average that is computed and does not refer to the math by which it is achieved. Thus the simple averaging in WPGMA produces a weighted result and the proportional averaging in UPGMA produces an unweighted result ('' see the working example''). Algorithm The UPGMA algorithm constructs a rooted tree ( dendrogram) that reflects the structure present in a pairwise similarity matrix (or a dissimilarity matrix). At each step, the nearest two clusters are combined into a higher-level cluster. The distance between any two clusters \mathcal and \mathcal, each of size (''i.e.'', cardinality) and , is taken to be the average of all distances d(x,y) between pairs of objects x in \m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command-line Interface
A command-line interface (CLI) is a means of interacting with software via command (computing), commands each formatted as a line of text. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user-friendly alternative to the non-interactive mode available with punched cards. For a long time, a CLI was the most common interface for software, but today a graphical user interface (GUI) is more common. Nonetheless, many programs such as operating system and software development utility software, utilities still provide CLI. A CLI enables automation, automating computer program, programs since commands can be stored in a scripting language, script computer file, file that can be used repeatedly. A script allows its contained commands to be executed as group; as a program; as a command. A CLI is made possible by command-line interpreters or command-line processors, which are programs that execute input commands. Alternatives to a CLI ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Batch Processing
Computerized batch processing is a method of running software programs called jobs in batches automatically. While users are required to submit the jobs, no other interaction by the user is required to process the batch. Batches may automatically be run at scheduled times as well as being run contingent on the availability of computer resources. History The term "batch processing" originates in the traditional classification of methods of production as job production (one-off production), batch production (production of a "batch" of multiple items at once, one stage at a time), and flow production (mass production, all stages in process at once). Early history Early computers were capable of running only one program at a time. Each user had sole control of the machine for a scheduled period of time. They would arrive at the computer with program and data, often on punched paper cards and magnetic or paper tape, and would load their program, run and debug it, and carry off thei ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Divergence (statistics)
In information geometry, a divergence is a kind of statistical distance: a binary function which establishes the separation from one probability distribution to another on a statistical manifold. The simplest divergence is squared Euclidean distance (SED), and divergences can be viewed as generalizations of SED. The other most important divergence is relative entropy (also called Kullback–Leibler divergence), which is central to information theory. There are numerous other specific divergences and classes of divergences, notably ''f''-divergences and Bregman divergences (see ). Definition Given a differentiable manifold M of dimension n, a divergence on M is a C^2-function D: M\times M\to [0, \infty) satisfying: # D(p, q) \geq 0 for all p, q \in M (non-negativity), # D(p, q) = 0 if and only if p=q (positivity), # At every point p\in M, D(p, p+dp) is a positive-definite quadratic form for infinitesimal displacements dp from p. In applications to statistics, the manifold M i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Similarity (geometry)
In Euclidean geometry, two objects are similar if they have the same shape, or if one has the same shape as the mirror image of the other. More precisely, one can be obtained from the other by uniformly scaling (geometry), scaling (enlarging or reducing), possibly with additional translation (geometry), translation, rotation (mathematics), rotation and reflection (mathematics), reflection. This means that either object can be rescaled, repositioned, and reflected, so as to coincide precisely with the other object. If two objects are similar, each is congruence (geometry), congruent to the result of a particular uniform scaling of the other. For example, all circles are similar to each other, all squares are similar to each other, and all equilateral triangles are similar to each other. On the other hand, ellipses are not all similar to each other, rectangles are not all similar to each other, and isosceles triangles are not all similar to each other. This is because two ellipse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Weighting
The process of frequency weighting involves emphasizing the contribution of particular aspects of a phenomenon (or of a set of data) over others to an outcome or result; thereby highlighting those aspects in comparison to others in the analysis. That is, rather than each variable in the data set contributing equally to the final result, some of the data is adjusted to make a greater contribution than others. This is analogous to the practice of adding (extra) weight to one side of a pair of scales in order to favour either the buyer or seller. While weighting may be applied to a set of data, such as epidemiological data, it is more commonly applied to measurements of light, heat, sound, gamma radiation, and in fact any stimulus that is spread over a spectrum A spectrum (: spectra or spectrums) is a set of related ideas, objects, or properties whose features overlap such that they blend to form a continuum. The word ''spectrum'' was first used scientifically in optics t ... [...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] |
Tree (data Structure)
In computer science, a tree is a widely used abstract data type that represents a hierarchical tree structure with a set of connected nodes. Each node in the tree can be connected to many children (depending on the type of tree), but must be connected to exactly one parent, except for the ''root'' node, which has no parent (i.e., the root node as the top-most node in the tree hierarchy). These constraints mean there are no cycles or "loops" (no node can be its own ancestor), and also that each child can be treated like the root node of its own subtree, making recursion a useful technique for tree traversal. In contrast to linear data structures, many trees cannot be represented by relationships between neighboring nodes (parent and children nodes of a node under consideration, if they exist) in a single straight line (called edge or link between two adjacent nodes). Binary trees are a commonly used type, which constrain the number of children for each parent to at most two. Whe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
