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TAXAassign specifications

Information


Unique identifier OMICS_21514
Name TAXAassign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A nucleotide sequence.
Operating system Unix/Linux
Programming languages Perl, Python, Shell (Bash)
Computer skills Advanced
Version 0.4
Stability Stable
Requirements
GNU Parallel, Blastn, NCBI's nt database, BioSQL, sqlite3 and MySQL
Maintained Yes

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TAXAassign in publications

 (2)
PMCID: 5919953
PMID: 29731741
DOI: 10.3389/fmicb.2018.00746

[…] estimates for each genome bin., open reading frames (orfs) of each genome bin were predicted by prodigal v2.6.3 in metagenomic mode. we implemented taxonomic assignments of the genome bins using taxaassign v.0.4 (https://github.com/umerijaz/taxaassign), with some modified codes to improve efficiency and accuracy. using the improved script, we used deduced amino acid sequence information […]

PMCID: 4960752
PMID: 27456340
DOI: 10.1186/s13104-016-2171-7

[…] then taxonomically classified against the rdp database using the standalone rdpclassifier v2.6 [] with the default–minwords option of 5. for species level assignment, we have used ncbi taxonomy and taxaassign (https://github.com/umerijaz/taxaassign). to find the phylogenetic distances between otus, we first multisequence aligned the otus against each other using mafft v7.040 [] and then used […]


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