Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.
Citations
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6,767 citations
Cites methods from "Fast UniFrac: facilitating high-thr..."
...We have previously shown, however, that patterns that were observed with de novo tree-making methods could be captured equally well using a “BLAST to reference tree” protocol (21) and then calculating community differences with UniFrac....
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2,966 citations
Cites methods from "Fast UniFrac: facilitating high-thr..."
...UniFrac analysis was performed using the Fast UniFrac Web interface, the Silva reference tree and an environment file mapping pyrosequencing reads to Silva reference sequences for each sample as described previously (Hamady et al., 2010)....
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2,622 citations
2,184 citations
Cites background or methods from "Fast UniFrac: facilitating high-thr..."
...Many early microbiome investigations are variants of Simulation A, and also used rarefying prior to calculating UniFrac distances [27]....
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...Rarefying is now an exceedingly common precursor to microbiome multivariate workflows that seek to relate sample covariates to sample-wise distance matrices [19,27,28]; for example, integrated as a recommended option in QIIME’s [29] beta_diversity_through_plots....
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References
88,255 citations
"Fast UniFrac: facilitating high-thr..." refers methods in this paper
...We demonstrate that using BLAST's (Altschul et al., 1990) megablast method to find the nearest neighbor of each short read in an existing library (in this case the Greengenes core set), recaptures the same patterns detected using the parsimony insertion method of ARB, and that these methods can be…...
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..., 2006) using BLAST’s megablast protocol (Altschul et al., 1990)....
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...We show below that the analysis of such large sequence sets is possible by assigning them to their closest relative in a phylogeny of the Greengenes core set (DeSantis et al., 2006) using BLAST's megablast protocol (Altschul et al., 1990)....
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...We demonstrate that using BLAST's (Altschul et al., 1990) megablast method to find the nearest neighbor of each short read in an existing library (in this case the Greengenes core set), recaptures the same patterns detected using the parsimony insertion method of ARB, and that these methods can be applied to pyrosequencing data with hundreds of thousands of sequences....
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...We show that using BLAST’s (Altschul et al., 1990) megablast method to find the nearest neighbor of each short read in an existing library (in this case the Greengenes core set), recaptures the same patterns detected using the parsimony insertion method of ARB, and that these methods can be applied to pyrosequencing data with hundreds of thousands of sequences....
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10,126 citations
"Fast UniFrac: facilitating high-thr..." refers background in this paper
...…Marhaver et al., 2008) assemblages important for understanding human health and disease (Frank et al., 2007; Li et al., 2008; Osman et al., 2008; Turnbaugh et al., 2006; Wen et al., 2008), bioremediation (Hiibel et al., 2008), and basic ecology and evolution (Balakirev et al., 2008; Bryant et…...
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..., 2008) assemblages important for understanding human health and disease (Turnbaugh et al., 2006; Frank et al., 2007; Li et al., 2008; Osman et al., 2008; Wen et al., 2008), bioremediation (Hiibel et al....
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9,593 citations
7,550 citations
"Fast UniFrac: facilitating high-thr..." refers background or methods in this paper
..., 2008b); (2) an analysis of how gut bacterial populations change in obese humans on fat-restricted and carbohydrate-restricted diets (Ley et al., 2006); (3) pyrosequencing studies of the human hand (Fierer et al....
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...We repeated the UniFrac analysis reported in Figure 1a of (Ley et al., 2006)....
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...The Global Environment dataset (Ley et al., 2008b) (99,801 sequences), the human obesity dataset (Ley et al., 2006)(18,348 sequences), and all unique pyrosequences from studies of the human hand, and the fecal microbiota of lean and obese twins (Fierer et al., 2008; Turnbaugh et al., 2009) (232,165…...
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...Hierarchical clustering based on UniFrac analysis of an ARB parsimony insertion tree showed that the bacterial lineages were remarkably constant within individuals over time, because samples from the same person generally clustered with each other rather than with samples from other people (Ley et al., 2006)....
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..., 2008b)(99 801 sequences), the human obesity dataset (Ley et al., 2006)(18 348 sequences), and all unique pyrosequences from studies of the human hand, and the fecal microbiota of lean and obese twins (Fierer et al....
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6,970 citations
"Fast UniFrac: facilitating high-thr..." refers background or methods in this paper
...…sequences), and all unique pyrosequences from studies of the human hand, and the fecal microbiota of lean and obese twins (Fierer et al., 2008; Turnbaugh et al., 2009) (232,165 unique sequences from 680,000 initial reads) were then searched against the Greengenes core set using megablast....
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..., 2006)(18 348 sequences), and all unique pyrosequences from studies of the human hand, and the fecal microbiota of lean and obese twins (Fierer et al., 2008; Turnbaugh et al., 2009) (232 165 unique sequences from 680 000 initial reads) were then searched against the Greengenes core set using megablast....
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...…on fat and carbohydrate restricted diets (Ley et al., 2006) (3) pyrosequencing studies of the human hand (Fierer et al., 2008), and of fecal microbiota of lean and obese twin pairs and their mothers (Turnbaugh et al., 2009), and (4) a PhyloChip study of citrus pathogens (Sagaram et al., 2009)....
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...…et al., 2007) and related efforts to study microbial communities occupying various human body habitats are revealing a surprising amount of diversity among individuals in skin (Fierer et al., 2008; Grice et al., 2008), gut (Turnbaugh et al., 2009), and mouth ecosystems (Nasidze et al., 2009)....
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...The levels of intra- and interpersonal variability observed within and between human body habitats (Frank et al., 2007; Fierer et al., 2008; Ley et al., 2008a; Turnbaugh et al., 2009) suggest that large sample sizes, including time series analyses, will be especially critical for understanding whether or not observed community structures are significantly associated with physiologic or pathophysiologic states....
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