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TreeBASE
TreeBASE was a repository of phylogenetic data published in scientific journals. In phylogenetic studies, research data are collected or generated, such as comparative observations (e.g. character state matrices or multiple sequence alignments) made on a set of taxa, metadata about these taxa, and the phylogenetic trees that are inferred to best describe the evolutionary relationships between the taxa. Mission The purpose of the TreeBASE project was to provide stable records and identifiers for these data, so that other workers can refer to their deposited data in their publication, and other scientists can locate the data and use them to verify the original research or to include or extend them in further analyses. History and funding The project was started in 1994, with funding from the US National Science Foundation. After this prototype, a redesign was initiated under the CIPRES project. This new version was released in March 2010 and has been supported by, among oth ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Phylogenetics
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by Computational phylogenetics, phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms. The tips of a phylogenetic tree can be living taxa or fossils, and represent the "end" or the present time in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and doe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Scientific Journal
In academic publishing, a scientific journal is a periodical publication intended to further the progress of science, usually by reporting new research. Content Articles in scientific journals are mostly written by active scientists such as students, researchers, and professors instead of professional journalists. There are thousands of scientific journals in publication, and many more have been published at various points in the past (see list of scientific journals). Most journals are highly specialized, although some of the oldest journals such as '' Nature'' publish articles and scientific papers across a wide range of scientific fields. Scientific journals contain articles that have been peer reviewed, in an attempt to ensure that articles meet the journal's standards of quality and scientific validity. Although scientific journals are superficially similar to professional magazines, they are actually quite different. Issues of a scientific journal are rarely read ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Maximum Parsimony (phylogenetics)
In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or miminizes the cost of differentially weighted character-state changes) is preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971. Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. However, although it is easy to ''score'' a phylogenetic tree (by counting the number of character-state changes), there is no algorithm to quickly ''generate'' the most-parsimonious tree. Instead, the most-parsimonious tree must be sought in "tree s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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 evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Taxa
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 system in ''Systema Naturae'', 10th edition (1758), as well as an unpublished work by Bernard and Antoine Laurent de Jussieu. The idea of a unit-based system of biological classification was first made widely available in 1805 in the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Metadata
Metadata is "data that provides information about other data", but not the content of the data, such as the text of a message or the image itself. There are many distinct types of metadata, including: * Descriptive metadata – the descriptive information about a resource. It is used for discovery and identification. It includes elements such as title, abstract, author, and keywords. * Structural metadata – metadata about containers of data and indicates how compound objects are put together, for example, how pages are ordered to form chapters. It describes the types, versions, relationships, and other characteristics of digital materials. * Administrative metadata – the information to help manage a resource, like resource type, permissions, and when and how it was created. * Reference metadata – the information about the contents and quality of Statistical data type, statistical data. * Statistical metadata – also called process data, may describe processes that collect, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Phylogenetic Tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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National Science Foundation
The National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health. With an annual budget of about $8.3 billion (fiscal year 2020), the NSF funds approximately 25% of all federally supported basic research conducted by the United States' colleges and universities. In some fields, such as mathematics, computer science, economics, and the social sciences, the NSF is the major source of federal backing. The NSF's director and deputy director are appointed by the President of the United States and confirmed by the United States Senate, whereas the 24 president-appointed members of the National Science Board (NSB) do not require Senate confirmation. The director and deputy director are responsible for administration, planning, budgeting and day-to-day operations of the foundation, whi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Contextual Query Language
Contextual Query Language (CQL), previously known as Common Query Language, is a formal language for representing queries to information retrieval systems such as search engines, bibliographic catalogs and museum collection information. Based on the semantics of Z39.50, its design objective is that queries be human readable and writable, and that the language be intuitive while maintaining the expressiveness of more complex query languages. It is being developed and maintained by the Z39.50 Maintenance Agency, part of the Library of Congress. Examples of query syntax Simple queries: dinosaur "complete dinosaur" title = "complete dinosaur" title exact "the complete dinosaur" Queries using Boolean logic: dinosaur or bird Palomar assignment and "ice age" dinosaur not reptile dinosaur and bird or dinobird (bird or dinosaur) and (feathers or scales) "feathered dinosaur" and (yixian or jehol) Queries accessing publication indexes: publicationYear 2.4 bioMass >= 100 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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National Evolutionary Synthesis Center
The United States National Evolutionary Synthesis Center (NESCent) is a scientific research center in Durham, North Carolina. Known by its acronym NESCent (which rhymes with “crescent”), the center’s goal is to promote collaborative, cross-disciplinary research in evolutionary biology. NESCent offers a range of fellowships for visiting scientists and educators and sponsors numerous scientific meetings each year. In its first 7 years, NESCent hosted nearly 4,200 visitors from more than 50 countries. Sponsored projects span the fields of systematics, paleontology, molecular evolution, phylogeography, comparative biology, evolutionary genetics, population biology and functional morphology, among others. Mission NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geogr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |