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Protocols

Tax4Fun specifications

Information


Unique identifier OMICS_08571
Name Tax4Fun
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Kathrin P. Aßhauer

Publication for Tax4Fun

Tax4Fun citations

 (26)
call_split

Oral microbiota reveals signs of acculturation in Mexican American women

2018
PLoS One
PMCID: 5918619
PMID: 29694348
DOI: 10.1371/journal.pone.0194100
call_split See protocol

[…] Tool (BLAST) [] to identify likely representative bacterial species. A rarefied OTU table with the associated centroid sequences is available in . Bacterial functional capabilities were imputed using Tax4Fun [], an algorithm using phylogenetic relationships to predict gene content, ultimately assigning functional pathways using the Kyoto Encyclopedia of Genes and Genomes [,]. […]

library_books

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

2018
Microbiome
PMCID: 5879801
PMID: 29609653
DOI: 10.1186/s40168-018-0449-9

[…] is is related to the difference in 16S rRNA gene copy numbers between species, yet this also accounts for other (marker) genes [, ]. Normalization of the 16S rRNA gene copy number was applied for the Tax4Fun analysis, as this is inherent to this software package []. However, no additional normalization to the copy number was applied, given the high variation in 16S rRNA gene copy number between sp […]

library_books

Taxa function robustness in microbial communities

2018
Microbiome
PMCID: 5833107
PMID: 29499759
DOI: 10.1186/s40168-018-0425-4

[…] o as the taxa-function relationship [], has many practical applications in the analysis of microbial communities. For example, this relationship is explicitly utilized by tools such as PICRUSt [] and Tax4Fun [] for predicting overall community gene content based on the community taxonomic profile and available reference genomes. Other studies have similarly used the taxa-function relationship to i […]

library_books

Gut Dysbiosis and Muscle Aging: Searching for Novel Targets against Sarcopenia

2018
PMCID: 5893006
PMID: 29686533
DOI: 10.1155/2018/7026198

[…] atabase, and Piphillin [], which has implemented an inference tool that works with any current genome database and has improved correlation and accuracy for clinical samples compared with PICRUSt and Tax4Fun [].Metagenomics is one of the most powerful tools available to unravel the complexity of gut microbiota. The integration of metagenomic data and other “omic” techniques (e.g., proteomics, meta […]

library_books

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

2018
Microbiome
PMCID: 5751889
PMID: 29298729
DOI: 10.1186/s40168-017-0391-2

[…] re defined by a Venn-diagram analysis using the software available at http://bioinformatics.psb.ugent.be.The OTU table was also used to predict the functional potential of bacterial communities using Tax4Fun []. Since Tax4Fun only recognized taxonomical data from the SILVA database, the OTUs previously obtained (as described in the paragraph ‘Metagenomic DNA extraction and metaphylogenomic analysi […]

call_split

Glyphosate Shapes a Dinoflagellate Associated Bacterial Community While Supporting Algal Growth as Sole Phosphorus Source

2017
Front Microbiol
PMCID: 5742145
PMID: 29312222
DOI: 10.3389/fmicb.2017.02530
call_split See protocol

[…] prediction of functional profiles of the bacterial community based on our 16S rRNA gene sequences, data from each treatment and the control were run through the newly developed open-source R package Tax4Fun (Aßhauer et al., ) after being processed with Qiime (based on SILVA). […]

Citations

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Tax4Fun institution(s)
Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany

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