ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time.
Citations
112 citations
105 citations
98 citations
Cites methods from "ESPRIT-Tree: hierarchical clusterin..."
...The objective of this work was to develop a simple and accurate method of classifying large datasets of pmoA sequences, a common marker for methanotrophic bacteria....
[...]
...The taxonomy-independent approach includes methods to compare sequence alignments and analyze operational taxonomic units (OTUs) based on sequence dissimilarity (Schloss and Handelsman, 2004; Cai and Sun, 2011)....
[...]
97 citations
Cites background from "ESPRIT-Tree: hierarchical clusterin..."
...A newer version of ESPRIT promises to be released soon that may dramatically lower this time [18]....
[...]
96 citations
Cites methods from "ESPRIT-Tree: hierarchical clusterin..."
...OTUs were calculated using ESPRIT-Tree [70]....
[...]
...Following Cai and Sun [70], the cutoff OTU level to best represent species level was determined using the normalized mutual information (NMI) criterion [71] on a subset of sequences that could be identified to species....
[...]
...Supporting Information Figure S1 Normalized mutual information (NMI) value between species and OTUs obtained for 30 difference levels using ESPRIT-Tree....
[...]
References
88,255 citations
37,524 citations
28,911 citations
"ESPRIT-Tree: hierarchical clusterin..." refers background in this paper
...In addition to microbial diversity estimation, there is currently increased interest in applying taxonomyindependent analysis to analyze millions of sequences for comparative microbial community analysis (11,12)....
[...]
...05 level 241 (7) 268 (6) 362 (11) 314 (9) peak NMI-species 402 (9) 400 (9) 590 (13) 314 (9) peak NMI-genus 190 (5) 176 (7) 216 (6) 243 (7)...
[...]
21,651 citations
17,405 citations