ESPRIT-Tree specifications

Information


Unique identifier OMICS_01445
Name ESPRIT-Tree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ESPRIT-Tree

ESPRIT-Tree in publications

 (18)
PMCID: 5486356
PMID: 28654083
DOI: 10.1038/sdata.2017.81

[…] step, before proceeding with the subsequent analyses. the number of reads remaining after this preprocessing step was 2,742,108., in the second analytical step, otu clustering was performed using esprit-tree version 11152011, which allows the same otu definition precision as standard hierarchical clustering procedures, but requires less execution time. the otus were classified using […]

PMCID: 5631090
PMID: 29018622
DOI: 10.7717/peerj.3889

[…] include pyronoise (), uparse (), dada2 () and unoise2 (), which attempt to infer correct biological sequences from noisy reads, and agglomerative methods implemented by dotur (), mothur () and esprit-tree () which assign reads to clusters without attempting to predict which sequences are correct., probably the best-known reference-based method is closed-reference clustering () […]

PMCID: 5193350
PMID: 28030619
DOI: 10.1371/journal.pone.0168860

[…] es instrument (ion torrent), and sequenced through pgm, ion torrent (life technologies)., raw data analysis was performed using a home-made pipeline composed of open-source softwares (mothur [], esprit-tree [], biome format []), databanks and home-made perl/python scripts, which were all implemented in galaxy []. briefly, the first step corresponded to a preprocessing step producing […]

PMCID: 4909783
PMID: 27379063
DOI: 10.3389/fmicb.2016.00933

[…] inference statistics, for the computation of fisher's α index (a semi-parametric index independent from the size of the sampling) and pielou's evenness. hierarchical clustering was carried out using esprit-tree (cai and sun, ). the output was used to compute operational taxonomic units (otus), rarefaction curves, as well as abundance-based coverage estimators (ace) and chao1 estimators, […]

PMCID: 4857090
PMID: 27147260
DOI: 10.1038/srep25255

[…] clustering steps. the sequences were then aligned against the silva database (release 102) provided with mothur. sequences with alignments under 100 bases were filtered out., in the second module, esprit-tree software was used for otu clustering. briefly, a partition tree was computed using the pbpcluster tool from the esprit-tree suite and a consensus sequence was generated for each otu […]


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ESPRIT-Tree institution(s)
Interdisciplinary Center for Biotechnology Research University of Florida, Gainesville, FL, USA

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