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Taxonerator specifications

Information


Unique identifier OMICS_15066
Name Taxonerator
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Groovy
Computer skills Medium
Stability Stable
Requirements
jMOTU, BLAST
Maintained Yes

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Maintainer


  • person_outline Mark Blaxter <>

Publication for Taxonerator

Taxonerator in publications

 (4)
PMCID: 5579096
PMID: 28878981
DOI: 10.1098/rsos.170315

[…] and phylogeny-based., alignment-based approaches use various measures of similarity between query and reference sequences based solely on their alignment. they are implemented in vamps [], taxonerator [] and crest [], or can be performed directly through blastn [] function of the ncbi server (https://blast.ncbi.nlm.nih.gov/blast.cgi). the performances of crest and blastn are evaluated […]

PMCID: 5136674
PMID: 27932928
DOI: 10.3897/BDJ.4.e10647

[…] alignment-based approach uses basic local alignment search tool (blast, ) algorithm implemented via ncbi server or as part of standalone software packages such as qiime (), lcaclassifier () or taxonerator (). the taxonomic placement of otus is based on whether the identity score (, , , , , ) or e-value () is above or below the predetermined similarity threshold. overlap range […]

PMCID: 4909793
PMID: 27178552
DOI: 10.1007/s00216-016-9595-8

[…] when searching a database of a particular size., a number of dedicated software pipelines exist that allow processing of metabarcoding data sets followed by taxonomic annotation, including jmotu and taxonerator [], clotu [], qiime [], mothur [] and uparse []. these software tools have been developed for studying microbial communities using the 16s rrna gene fragment, but they can also be used […]

PMCID: 3428669
PMID: 22574964
DOI: 10.1186/1471-2105-13-92

[…] of two approaches. (none of the programs mentioned in this paper combine all three approaches)., programs that primarily utilize sequence similarity search include carma [,], facs [], jmotu/taxonerator [], marta [], megan [], metaphyler [], mg-rast [], mtr [], and sort-items []. most of these programs employ blast (most commonly, blastx), and several incorporate some version […]

Taxonerator institution(s)
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
Taxonerator funding source(s)
Supported by the Leverhulme Trust (F/00158/BS).

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