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Esprit specifications


Unique identifier OMICS_01444
Name Esprit
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Esprit

Esprit in publications

PMCID: 5509686
PMID: 28706192
DOI: 10.1038/s41598-017-05262-8

[…] the gtr + i + g model was preferred for both loci according to mrmodeltest. distances were calculated using paup*4b. the genetic distances were used in hierarchical clustering (single linkage) in esprit, then we plotted genetic distance against the number of otus. the above phylogenetic and phenetic methods used two-genes. we additionally delineated based on coi only, since species-level […]

PMCID: 4776183
PMID: 26821041
DOI: 10.3390/v8020028

[…] an hpv genotype [,,]., quality sequences were clustered at 3% pairwise distance (representing 2% dissimilarity within variants [,,] plus 1% to more than compensate for sequencing errors) using esprit []. esprit generated a consensus sequence for each cluster representing an hpv genotype variant, and displayed the size of the cluster (number of sequences/cluster) reflecting the abundance […]

PMCID: 4505329
PMID: 26184838
DOI: 10.1038/srep12179

[…] quality value (qv 20) and length threshold of 100 bp. selected reads were then converted to fasta from fastq using fastx_toolkit (v0.0.13.2). subsequent preprocessing using the “preproc” module of esprit involved screening of only those reads which had intact 16s rdna universal primer sequence plus the barcode adaptor and the barcode. adaptor sequences were then trimmed; reads containing […]

PMCID: 4102501
PMID: 25033299
DOI: 10.1371/journal.pone.0102561

[…] 393–925). dereplication was obtained with the “unique.seqs” command of the mothur package (mothur 1.20.3). the distance matrices for each sample (3 triplicates combined) were calculated with esprit_pc (−f −r options) that uses a pairwise alignment approach . a mothur-compatible distance matrix was obtained with an in-house perlscript. mothur was used for clustering (command “cluster” […]

PMCID: 3998914
PMID: 24763141
DOI: 10.1371/journal.pcbi.1003594

[…] been developed for binning ssu sequences, most prominently hierarchical clustering algorithms (hca, implemented e.g. in mothur) and their heuristic approximations, such as uclust , cd-hit or the esprit suite of algorithms , . however, it has been noted that different clustering methods often provide highly inequivalent partitions of the same data, both quantitatively (with respect to total […]

Esprit institution(s)
Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA; Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA; Materials Technology Directorate, Air Force Technical Applications Center, Patrick AFB, FL, USA

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