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A dendrogram is a
Iris dendrogram
- Example of using a dendrogram to visualize the 3 clusters from
A dendrogram is a 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 o ...
representing a tree graph. This diagrammatic representation is frequently used in different contexts:
* in 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 ...
, it illustrates the arrangement of the clusters produced by the corresponding analyses.
* in computational biology
Computational biology refers to the use of techniques in computer science, data analysis, mathematical modeling and Computer simulation, computational simulations to understand biological systems and relationships. An intersection of computer sci ...
, it shows the clustering of gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s or samples, sometimes in the margins of heatmaps.
* in phylogenetics
In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
, it displays the evolution
Evolution is the change in the heritable Phenotypic trait, characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, re ...
ary relationships among various biological taxa
In biology, a taxon (back-formation from ''taxonomy''; : 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 ...
. In this case, the dendrogram is also called a 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 ...
.
The name ''dendrogram'' derives from the two ancient greek
Ancient Greek (, ; ) includes the forms of the Greek language used in ancient Greece and the classical antiquity, ancient world from around 1500 BC to 300 BC. It is often roughly divided into the following periods: Mycenaean Greek (), Greek ...
words (), meaning "tree", and (), meaning "drawing, mathematical figure".
Clustering example
For a clustering example, suppose that five taxa ( to ) have been clustered by UPGMA based on a matrix of genetic distances. Thehierarchical 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 ...
dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes represent the clusters to which the data belong, with the arrows representing the distance (dissimilarity). The distance between merged clusters is monotone, increasing with the level of the merger: the height of each node in the plot is proportional to the value of the intergroup dissimilarity between its two daughters (the nodes on the right representing individual observations all plotted at zero height).
See also
*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 s ...
* Distance matrices in phylogeny
* 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 ...
* MEGA, a freeware
Freeware is software, often proprietary, that is distributed at no monetary cost to the end user. There is no agreed-upon set of rights, license, or EULA that defines ''freeware'' unambiguously; every publisher defines its own rules for the free ...
for drawing dendrograms
* yEd, a freeware for drawing and automatically arranging dendrograms
* 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 o ...
References
Citations
Sources
* {{refendExternal links
Iris dendrogram
- Example of using a dendrogram to visualize the 3 clusters from
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 ...
using the "complete" method vs the real species category (using R).
Trees (data structures)
Statistical charts and diagrams
Graph drawing
Cluster analysis