A statistical method for evaluating systematic relationships

By R. Sokal, C. Michener. 1958

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Citations in the corpus

Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks (2011, background): “In both figures, proteins have been arranged by hierarchical clustering [23] to group potentially cross-talking systems together.”
Importance of shallow-water biotopes of a Caribbean bay for juvenile coral reef fishes: patterns in biotope association, community structure and spatial distribution (2000, methodology): “The average-linkage method (Sokal & Michener 1958) was used in combination with the Bray-Curtis coefficient.”
Recent developments in the MAFFT multiple sequence alignment program (2008, methodology): “It is more scalable than the conventional UPGMA algorithm with a time complexity of O ( N 2 ).”
Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives (2015, background): “The commonly usedmeasures of genetic distance (GD) or genetic similarity (GS) are (i) Nei and Li’s [82] coefficient (GDNL), (ii) Jaccard’s [83] coefficient (GDJ), (iii) simple matching coefficient (GDSM) [84], and (iv) modified Rogers’ distance (GDMR).”
Genetic Variation of Ethiopian Mustard (Brassica carinata A. Braun) Germplasm in Western Canada (2006, methodology): “…both of which are appropriate for two-state data, were computed from the binary matrix: the Sokal and Michener’s simple matching (SM) coefficient (Sokal and Michener 1958) and the Jaccard (J) coefficient (Jaccard 1908), which are defined as, SM ¼ aþ d n J ¼ a n d where a is the number of bands…”
Clustering Rules: A Comparison of Partitioning and Hierarchical Clustering Algorithms (2006, methodology): “The algorithm AGNES, as described by Kaufman and Rousseeuw [13] uses the group average method of Sokal and Michener [18].”
Hierarchical Clustering With Hard-Batch Triplet Loss for Person Re-Identification (2019, methodology): “Then, according to the unweighted average linkage clustering (unweighted pair-group method with arithmetic means, UPGMA) [19], we deﬁne the distance between clusters as: where C a i , C b j are two samples in the cluster C a , C b respectively. n a , n b represent the number of samples in C a , C b…”
MAFFT version 5: improvement in accuracy of multiple sequence alignment (2005, methodology): “A guide tree is constructed from the distances with the UPGMA method (12) with modified linkage (see supplementary material on our web page, http://www.”
Analysis of Genetic Diversity in Crop Plants—Salient Statistical Tools and Considerations (2003, background): “In general, GDJ and GDNL suffer cient (GDSM) (Sokal and Michener, 1958), and (iv) Modfrom unknown statistical distributions resulting from ified Rogers’ distance (GDMR).”
SSR-based assessment of genetic diversity in South American Vitis vinifera varieties (2006, methodology): “Similarity matrices, generated according to the Simple Matching coefficient [41] were used to perform cluster analyses by the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) [42] using the software NTSYS-pc [43].”
Application of phylogenetic networks in evolutionary studies. (2006, methodology): “…include ''neighbor joining'' (Saitou and Nei 1987), ''Bio-NJ'' (Gascuel 1997), ''Unweighted Pair Group Method with Arithmetic Mean (UPGMA)'' (Sokal and Michener 1958), ''the Buneman tree'' (Buneman 1971), the ''refined Buneman tree'' (Brodal et al. 2003), and standard consensus tree methods.”
STAMP: a web tool for exploring DNA-binding motif similarities (2007, methodology): “Finally, users may choose between two tree-building algorithms; an agglomerative method [UPGMA (11)] and a divisive method that is based on a self-organizing tree algorithm [SOTA (12)].”