Author: Anna R. Sjodin; Michael R. Willig; Simon J. Anthony
Title: Quantitative Delineation of Herpesviruses in Bats for use in Ecological Studies Document date: 2019_11_26
ID: 21ldw4lk_13
Snippet: To statistically support which OTU cutoff to use in subsequent analyses, the R package apcluster (Bodenhofer et al. 2011 ) was used to perform affinity propagation on the PID matrix of the total clone alignment. Affinity propagation is an algorithm that examines all data points in a similarity matrix to identify exemplars (Frey and Dueck 2007). The algorithm then clusters remaining data around an optimum number of exemplars by iteratively exchang.....
Document: To statistically support which OTU cutoff to use in subsequent analyses, the R package apcluster (Bodenhofer et al. 2011 ) was used to perform affinity propagation on the PID matrix of the total clone alignment. Affinity propagation is an algorithm that examines all data points in a similarity matrix to identify exemplars (Frey and Dueck 2007). The algorithm then clusters remaining data around an optimum number of exemplars by iteratively exchanging two types of "messages" between data points. In the context of viral sequences, the first type of message accumulates evidence for sequence k as an exemplar for sequence i, based on genetic distance between k and i (Frey and Dueck 2007). The second type of message reflects how many sequences besides i support k as the best choice of exemplar (Frey and Dueck 2007).
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