Dendrogram

A dendrogram is a diagram representing a tree. This diagrammatic

representation is frequently used in different contexts:

in hierarchical clustering, it illustrates the arrangement of

the clusters produced by the corresponding analyses.[4]
in computational biology, it shows the clustering of genes
or samples, sometimes in the margins of heatmaps.[5]
in phylogenetics, it displays the evolutionary
relationships among various biological taxa. In this case, Dendrogram of a hierarchical
clustering (UPGMA) with the height
the dendrogram is also called a phylogenetic tree.[6]
of the nodes (adapted from bacterial
The name dendrogram derives from the two ancient greek words 5S rRNA sequence data[1]).
δένδρον (déndron), meaning "tree", and γράμμα (grámma),
meaning "drawing, mathematical figure".[7][8]

Clustering example
For a clustering example, suppose that five taxa ( to ) 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
Dendrogram output for hierarchical
remaining nodes represent the clusters to which the data belong,
clustering of marine provinces using
with the arrows representing the distance (dissimilarity). The
presence / absence of sponge
distance between merged clusters is monotone, increasing with the
species.[2]
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 A dendrogram of the Tree of Life.
Hierarchical clustering This phylogenetic tree is adapted
MEGA, a freeware for drawing dendrograms from Woese et al. rRNA analysis.[3]
yEd, a freeware for drawing and automatically arranging The vertical line at bottom
dendrograms represents the last universal
common ancestor (LUCA).
 Taxonomy

References

Citations
1. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996).
Heatmap of RNA-Seq data showing
"Phylogenetic inference". In Hillis DM, Moritz C, Mable
two dendrograms in the left and top
BK (eds.). Molecular Systematics, 2nd edition.
margins.
Sunderland, MA: Sinauer. pp. 407–514.
ISBN 9780878932825.
2. Van Soest R, Boury-Esnault N, Vacelet J, Dohrmann M, Erpenbeck D, De Voogd N,
Santodomingo N, Vanhoorne B, Kelly M, Hooper J (2012). "Global Diversity of Sponges
(Porifera)" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338747). PLOS ONE. 7 (4):
e35105. Bibcode:2012PLoSO...735105V (https://ui.adsabs.harvard.edu/abs/2012PLoSO...7
35105V). doi:10.1371/journal.pone.0035105 (https://doi.org/10.1371%2Fjournal.pone.00351
05). PMC 3338747 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338747).
PMID 22558119 (https://pubmed.ncbi.nlm.nih.gov/22558119).
3. Woese, Carl R.; Kandler, O; Wheelis, M (1990). "Towards a natural system of organisms:
proposal for the domains Archaea, Bacteria, and Eucarya" (http://www.pnas.org/content/87/1
2/4576.full.pdf) (PDF). Proc Natl Acad Sci USA. 87 (12): 4576–4579.
Bibcode:1990PNAS...87.4576W (https://ui.adsabs.harvard.edu/abs/1990PNAS...87.4576W).
doi:10.1073/pnas.87.12.4576 (https://doi.org/10.1073%2Fpnas.87.12.4576). PMC 54159 (htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC54159). PMID 2112744 (https://pubmed.ncbi.nl
m.nih.gov/2112744).
4. Everitt, Brian (1998). Dictionary of Statistics (https://archive.org/details/cambridgediction00e
ver_0/page/96). Cambridge, UK: Cambridge University Press. p. 96 (https://archive.org/detai
ls/cambridgediction00ever_0/page/96). ISBN 0-521-59346-8.
5. Wilkinson, Leland; Friendly, Michael (May 2009). "The History of the Cluster Heat Map". The
American Statistician. 63 (2): 179–184. doi:10.1198/tas.2009.0033 (https://doi.org/10.1198%
2Ftas.2009.0033). S2CID 122792460 (https://api.semanticscholar.org/CorpusID:12279246
0).
6. "Phylogenetic tree (biology)" (https://www.britannica.com/science/phylogenetic-tree).
Encyclopedia Britannica. Retrieved 2018-10-22.
7. Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette.
ISBN 2010035283. OCLC 461974285 (https://www.worldcat.org/oclc/461974285).
8. Bailly, Anatole. "Greek-french dictionary online" (http://www.tabularium.be/bailly/).
www.tabularium.be. Retrieved October 20, 2018.

Sources
Galili, T. (2015). "dendextend: an R package for visualizing, adjusting and comparing trees
of hierarchical clustering" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817050).
Bioinformatics. 31 (22): 3718–3720. doi:10.1093/bioinformatics/btv428 (https://doi.org/10.10
 93%2Fbioinformatics%2Fbtv428). PMC 4817050 (https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC4817050). PMID 26209431 (https://pubmed.ncbi.nlm.nih.gov/26209431).

External links
Iris dendrogram (https://cran.r-project.org/web/packages/dendextend/vignettes/Cluster_Anal
ysis.html#the-3-clusters-from-the-complete-method-vs-the-real-species-category) - Example
of using a dendrogram to visualize the 3 clusters from hierarchical clustering using the
"complete" method vs the real species category (using R).

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