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Dendrogram

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Dendrogram of a hierarchical clustering (UPGMA) with the height of the nodes (adapted from bacterial 5S rRNA sequence data[1]).
Dendrogram output for hierarchical clustering of marine provinces using presence / absence of sponge species.[2]
A dendrogram of the Tree of Life. This phylogenetic tree is adapted from Woese et al. rRNA analysis.[3] The vertical line at bottom represents the last universal common ancestor (LUCA).
Heatmap of RNA-Seq data showing two dendrograms in the left and top margins.

A dendrogram is a diagram representing a tree. This diagrammatic representation is frequently used in different contexts:

The name dendrogram derives from the two ancient greek words 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 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

References

Citations

  1. ^ Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996). "Phylogenetic inference". In Hillis DM, Moritz C, Mable BK (eds.). Molecular Systematics, 2nd edition. 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)". PLOS ONE. 7 (4): e35105. Bibcode:2012PLoSO...735105V. doi:10.1371/journal.pone.0035105. PMC 3338747. PMID 22558119.
  3. ^ Woese, Carl R.; Kandler, O; Wheelis, M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya" (PDF). Proc Natl Acad Sci USA. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
  4. ^ Everitt, Brian (1998). Dictionary of Statistics. Cambridge, UK: Cambridge University Press. p. 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. CiteSeerX 10.1.1.165.7924. doi:10.1198/tas.2009.0033. S2CID 122792460.
  6. ^ "Phylogenetic tree (biology)". Encyclopedia Britannica. Retrieved 2018-10-22.
  7. ^ Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN 2010035283. OCLC 461974285.
  8. ^ Bailly, Anatole. "Greek-french dictionary online". www.tabularium.be. Retrieved October 20, 2018.

Sources

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Dendrogram
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