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Dendrogram
A dendrogram is a diagram representing a Tree (graph theory), tree graph. This diagrammatic representation is frequently used in different contexts: * in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. * in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heat map, heatmaps. * in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree. The name ''dendrogram'' derives from the two ancient greek words (), meaning "tree", and (), meaning "drawing, mathematical figure". Clustering example For a clustering example, suppose that five taxa (a to e) have been clustered by UPGMA based on a matrix of genetic distances. The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes repre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UPGMA Dendrogram Hierarchical
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 Robert R. Sokal, Sokal and Charles Duncan Michener, 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 (''#Second_distance_matrix_update, 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 distance matrix, 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 , ... [...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] |
Phylogenetic Tree
A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In other words, it 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. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape. Phylogenetic trees may be rooted or unrooted. In a ''rooted'' p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Diagram
A diagram is a symbolic Depiction, representation of information using Visualization (graphics), visualization techniques. Diagrams have been used since prehistoric times on Cave painting, walls of caves, but became more prevalent during the Age of Enlightenment, Enlightenment. Sometimes, the technique uses a Three-dimensional space, three-dimensional visualization which is then graphical projection, projected onto a two-dimensional surface. The word ''graphics, graph'' is sometimes used as a synonym for diagram. Overview The term "diagram" in its commonly used sense can have a general or specific meaning: * ''visual information device'' : Like the term "illustration", "diagram" is used as a collective term standing for the whole class of technical genres, including graphics, graphs, technical drawings and tables. * ''specific kind of visual display'' : This is the genre that shows qualitative data with shapes that are connected by lines, arrows, or other visual links. In scie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hierarchical Clustering
In data mining and statistics, hierarchical clustering (also called hierarchical cluster analysis or HCA) is a method of cluster analysis that seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into two categories: * Agglomerative: Agglomerative: Agglomerative clustering, often referred to as a "bottom-up" approach, begins with each data point as an individual cluster. At each step, the algorithm merges the two most similar clusters based on a chosen distance metric (e.g., Euclidean distance) and linkage criterion (e.g., single-linkage, complete-linkage). This process continues until all data points are combined into a single cluster or a stopping criterion is met. Agglomerative methods are more commonly used due to their simplicity and computational efficiency for small to medium-sized datasets . * Divisive: Divisive clustering, known as a "top-down" approach, starts with all data points in a single cluster and recursively splits the clu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cladogram
A cladogram (from Greek language, Greek ''clados'' "branch" and ''gramma'' "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an Phylogenetic tree, evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Charts And Diagrams
Statistics (from German: ', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industrial, or social problem, it is conventional to begin with a statistical population or a statistical model to be studied. Populations can be diverse groups of people or objects such as "all people living in a country" or "every atom composing a crystal". Statistics deals with every aspect of data, including the planning of data collection in terms of the design of surveys and experiments. When census data (comprising every member of the target population) cannot be collected, statisticians collect data by developing specific experiment designs and survey samples. Representative sampling assures that inferences and conclusions can reasonably extend from the sample to the population as a whole. An experimental study involves taking measurements of the sy ... [...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, e.g., including only woody plants with secondary growth, only plants that are usable as lumber, or only plants above a specified height. But wider definitions include taller palms, tree ferns, bananas, and bamboos. Trees are not a monophyletic taxonomic group but consist of a wide 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 trees reaching several thousand years old. Trees evolved around 400 million years ago, and it is estimated that there are around three trillion mature trees in the world currently. A tree typically has many secondary branches supported clear ... [...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] |
Taxonomy
image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme of classes (a taxonomy) and the allocation of things to the classes (classification). Originally, taxonomy referred only to the Taxonomy (biology), classification of organisms on the basis of shared characteristics. Today it also has a more general sense. It may refer to the classification of things or concepts, as well as to the principles underlying such work. Thus a taxonomy can be used to organize species, documents, videos or anything else. A taxonomy organizes taxonomic units known as "taxa" (singular "taxon"). Many are hierarchy, hierarchies. One function of a taxonomy is to help users more easily find what they are searching for. This may be effected in ways that include a library classification system and a Taxonomy for search e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
