RDP4 protocols

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RDP4 specifications

Information


Unique identifier OMICS_13036
Name RDP4
Alternative name Recombination Detection Program
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data DNA sequence, alignment, ORF positions and names
Input format PHYLIP, GDE, FASTA, CLUSTAL, GCG, NEXUS, MEGA, DNAMAN, rdp, pdb
Output data Results summary
Output format rdp, csv
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 4.95
Stability Beta
Maintained No
Wikipedia https://en.wikipedia.org/wiki/Recombination_detection_program

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Publications for Recombination Detection Program

RDP4 in pipelines

 (76)
2018
PMCID: 5803923
PMID: 29415728
DOI: 10.1186/s12917-018-1345-z

[…] phylogenetic tree based on complete genome as well as cap gene and rep gene. in the recombination events, possible breakpoint were identified using two programs based on different approaches: the rdp4 (http://web.cbio.uct.ac.za/~darren/rdp.html) [] and simplot(http://sray.med.som.jhmi.edu/raysoft) []. the rdp tests the recombination events by six methods (geneconv, bootscan, maxchi, chimaera, […]

2018
PMCID: 5831051
PMID: 29489860
DOI: 10.1371/journal.pone.0192565

[…] the subsequent analyses less computationally demanding and will assure better model convergence as suggested elsewhere [–]. recombination events in the selected sequences were not detected using recombination detection program version 3.0 []. finally, we used tempest version 1.5.1 [] to explore the presence of temporal structure in the sequence data and estimated a positive correlation […]

2018
PMCID: 5837103
PMID: 29505612
DOI: 10.1371/journal.pone.0193892

[…] settings, except for ignoring all the sites with gaps. all novel sequences representing srlv isolates reported in this study are available under genbank accession numbers ky864978–ky865033., the recombination detection program, version 3.44 (rdp3) was used to detect possible recombination events []. rdp3 provides access to seven primary exploratory recombination signal detection methods. […]

2018
PMCID: 5854769
PMID: 29545304
DOI: 10.1128/genomeA.01457-17

[…] size, was identified as tomv by blastn analysis. it was found to be the full-length genome sequence upon further inspection. the zimbabwe tomv isolate was analyzed for recombination events using the rdp4 program (). the full-genome and coat protein (cp) sequences of the zimbabwe tomv isolate and other tomv isolates retrieved from genbank were subjected to maximum likelihood phylogenetic analysis […]

2018
PMCID: 5877446
PMID: 29607253
DOI: 10.7717/peerj.4476

[…] model, and a bootstrap confidence value of 1,000 replicates., to detect putative recombination events in pcv2, recombinant strains were investigated on the complete genome database using a recombination detection program (rdp v.4.24) () as described by . briefly, seven methods (rdp, geneconv, bootscan, maxchi, chimera, siscan, and 3seq) were used for preliminary scan and only events […]


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RDP4 in publications

 (324)
PMCID: 5954121
PMID: 29765018
DOI: 10.1038/s41467-018-04217-5

[…] parental strains or enumerate distinct recombination events. among the programs that provide a list of detected recombinants, including their potential breakpoints and parental strains, is the suite rdp4, which, in addition to implementing the recombination detection program (rdp) approach, includes several other existing tools, providing corroboration of findings across the different methods. […]

PMCID: 5946465
PMID: 29747679
DOI: 10.1186/s13104-018-3395-5

[…] percentages of pairwise identity among the aligned nucleotide and protein sequences were calculated using matgat v.2.03 []. putative reassortment and recombination events were predicted by recombination detection program (rdp4 v.4.80) [] using several algorithms on the muscle alignment file of concatenated full-length genome sequences, created with mega7., insv-up01 produced typical […]

PMCID: 5941070
PMID: 29739906
DOI: 10.1128/mBio.02109-17

[…] replicates) was used to calculate branch support. only support values of >90% were considered statistically significant. to determine possible recombination events, sequences were analyzed using recombination detection program 3beta27 (rdp3beta27) (). new phylogenetic analyses were performed according to the proposed breakpoint position(s) in those suspected recombinant sequences to confirm […]

PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] be observed (data not shown), potentially due to the high number of variant positions present. to further examine potential recombination, six recombination detection tests, namely geneconv, maxchi, recombination detection program (rdp), bootscan, 3seq and siscan were used to analyse snv-derived alignments. a total of 83 potential recombination events were detected in the concatenated snv […]

PMCID: 5915611
PMID: 29691483
DOI: 10.1038/s41598-018-24870-6

[…] within the 2c coding region (parental relationship inferred from a group of o/mya-98(b) viruses) (fig. ). event 6: recent recombinant a/sea-97 a/hy/cha/2013 (kt968663), was not detected by rdp4, but was identified by the phylogenetic reconstruction of the recombination-free segments and simplot analysis that revealed high identity with lineage o/mya-98(b) in 2c and 3c-3d coding regions […]


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RDP4 institution(s)
Department of Integrative Biomedical Sciences, Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Statistics, University of Oxford, Oxford, UK
RDP4 funding source(s)
This work was supported by the South African National Research Foundation; the University of Cape Town, the Polyomielitis Research Foundation, and the Carnergie Corporation; and by the United States National Institutes of Health (AI090970, U01GM110749, and AI100665).

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