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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] |
Graph-theoretical Tree
In graph theory, a tree is an undirected graph in which any two vertices are connected by ''exactly one'' path, or equivalently a connected acyclic undirected graph. A forest is an undirected graph in which any two vertices are connected by ''at most one'' path, or equivalently an acyclic undirected graph, or equivalently a disjoint union of trees. A polytreeSee . (or directed tree or oriented treeSee .See . or singly connected networkSee .) is a directed acyclic graph (DAG) whose underlying undirected graph is a tree. A polyforest (or directed forest or oriented forest) is a directed acyclic graph whose underlying undirected graph is a forest. The various kinds of data structures referred to as trees in computer science have underlying graphs that are trees in graph theory, although such data structures are generally rooted trees. A rooted tree may be directed, called a directed rooted tree, either making all its edges point away from the root—in which case it is called an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Horizontal Gene Transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created Bactericide, pesticides and in the evolution, maintenance, and transmission of virulence. It often involves Temperateness (virology), temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Trees (data Structures)
In botany, a tree is a perennial plant with an elongated stem, or trunk, usually supporting branches and leaves. In some usages, the definition of a tree may be narrower, including only woody plants with secondary growth, plants that are usable as lumber or plants above a specified height. In wider definitions, the taller palms, tree ferns, bananas, and bamboos are also trees. Trees are not a taxonomic group but include a variety of plant species that have independently evolved a trunk and branches as a way to tower above other plants to compete for sunlight. The majority of tree species are angiosperms or hardwoods; of the rest, many are gymnosperms or softwoods. Trees tend to be long-lived, some reaching several thousand years old. Trees have been in existence for 370 million years. It is estimated that there are some three trillion mature trees in the world. A tree typically has many secondary branches supported clear of the ground by the trunk. This trunk typically co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Smart Game Format
The Smart Game Format (SGF) is a computer file format used for storing records of board games. Go is the game that is most commonly represented in this format and is the default. SGF was originally created under a different name by Anders Kierulf for his SmartGO program. The current version of the format is 4. The main purposes of SGF are to store records of played games and to provide features for storing annotated and analyzed games (e.g. board markup, variations). It is a text-only, tree-based format. The tree structure makes the addition of variations simple. It is also text-based instead of binary for the sake of portability. Games stored in SGF format can easily be emailed, posted or processed with text-based tools. Most Internet Go servers and Go software from 1990 support this format. About the format An SGF file is composed of pairs of properties and property values, each of which describes a feature of the game. A partial list of properties appears below. T ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
T-REX (Webserver)
T-REX (Tree and Reticulogram Reconstruction) is a freely available web server, developed at the department of Computer Science of the Université du Québec à Montréal, dedicated to the inference, validation and visualization of phylogenetic trees and phylogenetic networks. The T-REX web server allows the users to perform several popular methods of phylogenetic analysis as well as some new phylogenetic applications for inferring, drawing and validating phylogenetic trees and networks. Phylogenetic inference The following methods for inferring and validating phylogenetic trees using distances are available: Neighbor joining (NJ),NINJA large-scale Neighbor Joining''k'') = exp(-''k'')), and the constant a is a tuning factor accounting for the deviation intensity (as described in Guindon and Gascuel (2002), the value of a was set to 0.8). The random trees generated by this procedure have depth of O(log (''n'')). References {{Reflist die External links Official T-REX Web server p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PhyloXML
PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language. A shortcoming of current formats for describing phylogenetic trees (such as Nexus and Newick/New Hampshire) is a lack of a standardized means to annotate tree nodes and branches with distinct data fields (which in the case of a basic species tree might be: species names, branch lengths, and possibly multiple support values). Data storage and exchange is even more cumbersome in studies in which trees are the result of a reconciliation of some kind: * gene-function studies (requires annotation of nodes with taxonomic information as well as gene names, and possibly gene-duplication data) * evolution of host-parasite interactions (requires annotation of tree nodes with taxonomic information for both host and parasite) * phylogeographic studies (requires annotation of tree nodes with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
T-REX (webserver)
T-REX (Tree and Reticulogram Reconstruction) is a freely available web server, developed at the department of Computer Science of the Université du Québec à Montréal, dedicated to the inference, validation and visualization of phylogenetic trees and phylogenetic networks. The T-REX web server allows the users to perform several popular methods of phylogenetic analysis as well as some new phylogenetic applications for inferring, drawing and validating phylogenetic trees and networks. Phylogenetic inference The following methods for inferring and validating phylogenetic trees using distances are available: Neighbor joining (NJ),NINJA large-scale Neighbor Joining''k'') = exp(-''k'')), and the constant a is a tuning factor accounting for the deviation intensity (as described in Guindon and Gascuel (2002), the value of a was set to 0.8). The random trees generated by this procedure have depth of O(log (''n'')). References {{Reflist die External links Official T-REX Web server p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rice University
William Marsh Rice University (Rice University) is a Private university, private research university in Houston, Houston, Texas. It is on a 300-acre campus near the Houston Museum District and adjacent to the Texas Medical Center. Rice is ranked among the top universities in the United States. Opened in 1912 as the Rice Institute after the murder of its namesake William Marsh Rice, Rice is a research university with an undergraduate focus. Its emphasis on undergraduate education is demonstrated by its 6:1 student-faculty ratio. The university has a Research I university, very high level of research activity, with $156 million in sponsored research funding in 2019. Rice is noted for its applied science programs in the fields of artificial heart research, structural chemical analysis, signal processing, space science, and nanotechnology. Rice has been a member of the Association of American Universities since 1985 and is Carnegie Classification of Institutions of Higher Education ... [...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] |
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] |
Integer
An integer is the number zero (), a positive natural number (, , , etc.) or a negative integer with a minus sign (−1, −2, −3, etc.). The negative numbers are the additive inverses of the corresponding positive numbers. In the language of mathematics, the set of integers is often denoted by the boldface or blackboard bold \mathbb. The set of natural numbers \mathbb is a subset of \mathbb, which in turn is a subset of the set of all rational numbers \mathbb, itself a subset of the real numbers \mathbb. Like the natural numbers, \mathbb is countably infinite. An integer may be regarded as a real number that can be written without a fractional component. For example, 21, 4, 0, and −2048 are integers, while 9.75, , and are not. The integers form the smallest group and the smallest ring containing the natural numbers. In algebraic number theory, the integers are sometimes qualified as rational integers to distinguish them from the more general algebraic integers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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