TACOA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TACOA
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Tool usage distribution map

This map represents all the scientific publications referring to TACOA per scientific context
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TACOA specifications

Information


Unique identifier OMICS_01467
Name TACOA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for TACOA

TACOA citations

 (16)
library_books

Current Knowledge and Computational Techniques for Grapevine Meta Omics Analysis

2018
Front Plant Sci
PMCID: 5767322
PMID: 29375610
DOI: 10.3389/fpls.2017.02241

[…] d (Xia et al., ). In compositional-based approaches, k-mer frequency measurements are used to classify metagenomic reads. Methods such as TETRA (Teeling et al., ), CompostBin (Chatterji et al., ) and TACOA (Diaz et al., ) organize sequences in clusters (k-mer frequency is used to build a feature vector to compute distances between reads). Next, they assign an unique taxon to each cluster through a […]

library_books

EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST

2017
Sci Rep
PMCID: 5573435
PMID: 28842700
DOI: 10.1038/s41598-017-09947-y

[…] duced by IMMs to improve the accuracy of using BLAST alone. Traditional kNN is faced with the curse of dimensionality problem when the dimensionality of k-mer profiles is high. To solve this problem, TACOA introduces a Gaussian kernel to extend the traditional kNN and applies kNN for fragments classification. PhyloPythia takes the oligonucleotide composition of variable-length genome fragments as […]

library_books

Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes

2016
Front Microbiol
PMCID: 4828583
PMID: 27148174
DOI: 10.3389/fmicb.2016.00469

[…] ve and accurate, but suffer primarily due to the time required to generate the BLAST or BLAT alignments. The composition-based or marker-gene based approaches, such as Phylopythia (McHardy et al., ), TACOA (Diaz et al., ), PhymmBL (Brady and Salzberg, ), and MetaPhlAn (Segata et al., ) are several times faster in execution but provide limited classification accuracy and efficiency. However, given […]

library_books

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

2015
BMC Bioinformatics
PMCID: 4634789
PMID: 26537885
DOI: 10.1186/s12859-015-0788-5

[…] to the way we evaluated methods, the most conservative methods will show the highest sensitivity and precision, but may not be making classifications at specific enough taxonomic ranks to be useful. TACOA, for example, shows high sensitivity and precision, yet makes classifications at very high taxonomic ranks that would not be useful for most researchers.Not surprisingly, the sensitivity increas […]

library_books

MLgsc: A Maximum Likelihood General Sequence Classifier

2015
PLoS One
PMCID: 4492669
PMID: 26148002
DOI: 10.1371/journal.pone.0129384

[…] ing techniques to classify queries based on properties of the sequences, such as frequencies of fixed-length words (k-mers). The Ribosomal Database Project (RDP) classifier [] as well as SCIMM [] and TACOA [] belong to this category. Finally, phylogeny-based methods classify by placing the query in a phylogenetic tree along with references and examining its relatives. To this class belong, among o […]

library_books

Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier

2015
Evol Bioinform Online
PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] thod using generic features such as their 16S rRNA, GC content, and other oligonucleotide frequencies.8 Currently, there are several composition-based methods: PhyloPythia,9 Phylo-PythiaS,10 Phymm,11 TACOA,12 S-GSOM,13 NBC,14 RAIphy,15 KNNLog,16 Taxsom,17 and MetaCluster 3.0.18 However, at lower taxonomic levels, such as genus and species levels, most of these composition-based methods cannot achi […]


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TACOA institution(s)
Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

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