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Associated diseases

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TaxSOM specifications

Information


Unique identifier OMICS_01468
Name TaxSOM
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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Maintainer


  • person_outline Hanno Teeling <>

Publication for TaxSOM

TaxSOM in publications

 (4)
PMCID: 4309676
PMID: 25673967
DOI: 10.4137/EBO.S20523

[…] 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 achieve the prediction accuracy required […]

PMCID: 3794082
PMID: 24124405
DOI: 10.5808/GI.2013.11.3.102

[…] oligonucleotide composition []. among the above, nbc and phymm are suitable for classifying short reads generated from ngs sequencers. the popular tools employing unsupervised learning are tacoa and taxsom. tacoa introduced a kernelized k-nearest neighbor approach to cluster the reads [], while taxsom uses batch-learning self-organizing maps (blsoms) and growing soms (gsoms) to generate […]

PMCID: 3252642
PMID: 22232619
DOI: 10.3389/fmicb.2011.00268

[…] reads for tle) were used for de novo metagenomic assembly in geneious with default parameters for “medium sensitivity.” taxonomic classification of whc2b contigs > 2 kb was conducted with the taxsom server (weber et al., ) with a pre-calculated model for all archaea and bacteria. automated annotation of open reading frames in contig whc2b.c1 was performed by the rast server (aziz et al., […]

PMCID: 3300000
PMID: 22180538
DOI: 10.1093/nar/gkr1204

[…] tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. the proposed method has a demonstrated improvement over phylopythia, s-gsom, tacoa and taxsom on all three benchmarks that were used for evaluation in this study. the proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern […]


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TaxSOM institution(s)
Max Planck Institute for Marine Microbiology, Bremen, Germany

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