|
Robinson–Foulds Metric
The Robinson–Foulds or symmetric difference metric, often abbreviated as the RF distance, is a simple way to calculate the distance between phylogenetic trees. It is defined as ( + ) where is the number of partitions of data implied by the first tree but not the second tree and is the number of partitions of data implied by the second tree but not the first tree (although some software implementations divide the RF metric by 2 and others scale the RF distance to have a maximum value of 1). The partitions are calculated for each tree by removing each branch. Thus, the number of eligible partitions for each tree is equal to the number of branches in that tree. RF distances have been criticized as biased, but they represent a relatively intuitive measure of the distances between phylogenetic trees and therefore remain widely used (the original 1981 paper describing Robinson-Foulds distances was cited more than 200 times in 2019 based on Google Scholar). Nevertheless, the biases inhe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Trees
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 to be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Google Scholar
Google Scholar is a freely accessible web search engine that indexes the full text or metadata of scholarly literature across an array of publishing formats and disciplines. Released in beta in November 2004, the Google Scholar index includes peer-reviewed online academic journals and books, conference papers, theses and dissertations, preprints, abstracts, technical reports, and other scholarly literature, including court opinions and patents. Google Scholar uses a web crawler, or web robot, to identify files for inclusion in the search results. For content to be indexed in Google Scholar, it must meet certain specified criteria. An earlier statistical estimate published in PLOS One using a mark and recapture method estimated approximately 80–90% coverage of all articles published in English with an estimate of 100 million.''Trend Watch'' (2014) Nature 509(7501), 405 – discussing Madian Khabsa and C Lee Giles (2014''The Number of Scholarly Documents on the Public Web'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 int ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metric (mathematics)
In mathematics, a metric space is a set together with a notion of ''distance'' between its elements, usually called points. The distance is measured by a function called a metric or distance function. Metric spaces are the most general setting for studying many of the concepts of mathematical analysis and geometry. The most familiar example of a metric space is 3-dimensional Euclidean space with its usual notion of distance. Other well-known examples are a sphere equipped with the angular distance and the hyperbolic plane. A metric may correspond to a metaphorical, rather than physical, notion of distance: for example, the set of 100-character Unicode strings can be equipped with the Hamming distance, which measures the number of characters that need to be changed to get from one string to another. Since they are very general, metric spaces are a tool used in many different branches of mathematics. Many types of mathematical objects have a natural notion of distance and t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetics
In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, 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, protein Amino acid, amino acid sequences, or Morphology (biology), 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 un ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PHYLIP
PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). It consists of 65 portable programs, i.e., the source code is written in the programming language C. As of version 3.696, it is licensed as open-source software; versions 3.695 and older were proprietary software freeware. Releases occur as source code, and as precompiled executables for many operating systems including Windows (95, 98, ME, NT, 2000, XP, Vista), Mac OS 8, Mac OS 9, OS X, Linux ( Debian, Red Hat); and FreeBSD from FreeBSD.org. Full documentation is written for all the programs in the package and is included therein. The programs in the phylip package were written by Professor Joseph Felsenstein, of the Department of Genome Sciences and the Department of Biology, University of Washington, Seattle. Methods (implemented by each program) that are available in the package include parsimony, distance matrix, and likelihood met ... [...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] |
Quartet Distance
The quartet distance is a way of measuring the distance between two phylogenetic trees. It is defined as the number of subsets of four leaves that are not related by the same topology in both trees. Computing the quartet distance The most straightforward computation of the quartet distance would require O(N^4) time, where N is the number of leaves in the trees. For binary trees, better algorithm In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...s have been found to compute the distance in * O(N^2) time * O(N \log^2 N) time and * O(N \log N) time Gerth Stølting Brodal ''et al.'' found an algorithm that takes O(D N \log N) time to compute the quartet distance between two multifurcating trees when D is the maximum degree of the trees, which iaccessiblein C, perl, and the R packa ... [...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] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ... [...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] |
