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RAIphy specifications


Unique identifier OMICS_01464
Name RAIphy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.0.0
Stability Stable
Source code URL http://bioinfo.unl.edu/downloads/RAIphy.zip
Maintained Yes




No version available

Publication for RAIphy

RAIphy citations


Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities

BMC Bioinformatics
PMCID: 5751639
PMID: 29297282
DOI: 10.1186/s12859-017-1901-8

[…] genomes for classification and as such they utilize less computational resources. taxy [] uses k-mer distribution in reference genomes and metagenomes and a mixture model to identify the organisms. raiphy [] uses k-mers to build relative abundance index, classification metric and the iterative algorithm to refine the model and estimate the abundance. composition-based method have been proven […]


Dissemination of antibiotic resistance genes from antibiotic producers to pathogens

Nat Commun
PMCID: 5467266
PMID: 28589945
DOI: 10.1038/ncomms15784

[…] three proteins are harboured by pathogens, including the well-known aminoglycoside-inactivating phosphotransferase aph(3″) (wp_031942890.1)., by analysing dna sequence composition signatures using raiphy, we found that two of the proteobacterial proteins, chloramphenicol exporter cmx (wp_005297378.1) and lincomycin exporter lmra (wp_038989331.1), may have been recently transferred […]


Metagenomic Analysis of a Complex Community Present in Pond Sediment

J Genomics
PMCID: 5362764
PMID: 28348642
DOI: 10.7150/jgen.16685

[…] was used to filter the assembled sequences . the cutoff for minimum contig length was kept >200 bp in order to ensure a reasonable length for predicted orfs ., assembled contigs were binned using raiphy and also by comparing the same to the ncbi non-redundant protein database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr, june, 2015) using blastx (e-value = 1e-10) . the metagenome analyzer (megan […]


Expanding the Repertoire of Carbapenem Hydrolyzing Metallo ß Lactamases by Functional Metagenomic Analysis of Soil Microbiota

Front Microbiol
PMCID: 5184135
PMID: 28082950
DOI: 10.3389/fmicb.2016.01985

[…] seven subclass b3 (crd3-1, pedo-1, grd33-1, esp-2, alg6-1, alg11-1, and dht2-1). except pedo-1 and esp-2, these enzymes were distantly related to any previously described mbls (33 to 59% identity). raiphy analysis indicated that six enzymes (crd3-1, grd23-1, dht2-1, spn79-1, alg6-1, and alg11-1) originated from proteobacteria, two (pedo-1 and esp-2) from bacteroidetes and one (grd33-1) […]


Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes

Sci Rep
PMCID: 5006077
PMID: 27577999
DOI: 10.1038/srep32322

[…] by genetic complementation of temperature-sensitive (ts) fabi or fabg mutants of e. coli, respectively (). a higher diversity of tcs resistance determinants was observed in as compared to ics ()., raiphy (relative abundance index phylogenetic analysis)-based taxonomic assignment of metagenomic clones revealed that the majority belonged to the phylum proteobacteria (). the metagenomic […]


Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog

Front Microbiol
PMCID: 4602129
PMID: 26528253
DOI: 10.3389/fmicb.2015.01087

[…] with newbler (roche ver. 2.6). contigs and orphaned reads were annotated using the mg-rast server (), phylogenetic placement of reads and contigs was performed using both phylopythias () and raiphy (). sequence data has been deposited at mgrast under project number 14718 (mg-rast id for bcm sample 4452826.3 and control 4452824.3)., as previously described, a dose mediated response […]

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RAIphy institution(s)
Department of Electrical Engineering, University of Nebraska Lincoln, Lincoln, NE, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
RAIphy funding source(s)
Supported in part by a grant from the National Institutes of Health under grant K25AI068151.

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