A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
Citations
2,360 citations
Cites background from "A DNA-Based Registry for All Animal..."
...It raises the controversial idea that many species may become known by a number derived from barcoding and not—or not only—from conventional descriptions (123)....
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2,252 citations
Cites background from "A DNA-Based Registry for All Animal..."
...…identifying clusters, and it has previously been adapted for diverse biological problems, including orthology assignments (Enright et al. 2002), detection of operational taxonomic units (Ratnasingham & Hebert 2013), and identification of co-occurring associations among microbes (Faust et al. 2012)....
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685 citations
609 citations
535 citations
Cites background from "A DNA-Based Registry for All Animal..."
...This and previous studies (Monaghan et al., 2009; Esselstyn et al., 2012; Ratnasingham and Hebert, 2013; Tang et al., 2014) suggest that single-locus barcoding methods provide meaningful clusters, close to taxonomically acknowledged species....
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References
57,055 citations
"A DNA-Based Registry for All Animal..." refers methods in this paper
...N N Sequences: Sequences are represented in three ways: 1) as a histogram of distances generated from all pairwise comparisons within the BIN together with a representative of the nearest neighbouring BIN, 2) as a neighbor-joining tree [53] and as a haplotype similarity network diagram....
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17,350 citations
Additional excerpts
...Algorithms based on single linkage clustering [20–23] have been widely used to quantify microbial diversity....
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14,144 citations
"A DNA-Based Registry for All Animal..." refers methods in this paper
...RESL defines the boundaries of each OTU selected for analysis by generating clusters using a range of values for the inflation parameter in MCL and then selects that which maximizes the Silhouette index [37]....
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...The final step selects the optimal partitions for OTUs based on the Silhouette index, a cluster validation method that measures how tightly clusters are integrated [37]....
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14,075 citations
"A DNA-Based Registry for All Animal..." refers background in this paper
...A profile Hidden Markov Model [43] of the COI protein [44] aligns the input sequences....
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...If a sequence meets these quality requirements, it is then checked for reading frame shifts as indicated by stop codons or improbable peptides given the COI profile [44]....
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13,100 citations
"A DNA-Based Registry for All Animal..." refers methods in this paper
...Prior to phylogeny reconstruction, the most appropriate model of evolution was separately estimated for each dataset from alignments using jModelTest [50]....
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