A dendrogram is a
diagram
A diagram is a symbolic representation of information using visualization techniques. Diagrams have been used since prehistoric times on walls of caves, but became more prevalent during the Enlightenment. Sometimes, the technique uses a three ...
representing a
tree
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 ...
. 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
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s or samples, sometimes in the margins of
heatmaps.
* in
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 ...
, it displays the
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
ary 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
Ancient Greek includes the forms of the Greek language used in ancient Greece and the ancient world from around 1500 BC to 300 BC. It is often roughly divided into the following periods: Mycenaean Greek (), Dark Ages (), the Archaic pe ...
words (), meaning "tree", and (), meaning "drawing, mathematical figure".
Clustering example
For a clustering example, suppose that five taxa (
to
) have been clustered by
UPGMA
UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. The method is generally attributed to Sokal and Michener.
The UPGMA method is similar to its ''weighted'' variant, the ...
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 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
*
Distance matrices in phylogeny
*
Hierarchical clustering
*
MEGA, a
freeware
Freeware is software, most 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 ...
for drawing dendrograms
*
yEd
yEd is a general-purpose diagramming program with a multi-document interface.
It is a cross-platform application written in Java that runs on Windows, Linux, Mac OS, and other platforms that support the Java Virtual Machine.
It is released und ...
, a freeware for drawing and automatically arranging dendrograms
*
Taxonomy
References
Citations
Sources
*
{{refend
External links
Iris dendrogram- Example of using a dendrogram to visualize the 3 clusters from
hierarchical clustering using the "complete" method vs the real species category (using
R).
Trees (data structures)
Statistical charts and diagrams
Graph drawing
Cluster analysis