RDP4 pipeline

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 Yes
Wikipedia https://en.wikipedia.org/wiki/Recombination_detection_program

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Documentation


Maintainer


  • person_outline Darren P Martin <>

Publications for Recombination Detection Program

RDP4 IN pipelines

 (11)
2018
PMCID: 5799169
PMID: 29403002
DOI: 10.1038/s41598-018-19312-2

[…] of the 90 circulating recombinant forms (crf), including the 43 crfs with subtype b sequences at pol. this was confirmed by analyzing recombination breakpoints in our hiv-1bpr alignment using the rdp4 package employing the default parameters35. recombination signals detected with p < 0.05 by at least four different methods were considered as positive. recombination breakpoints […]

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 [52–54]. recombination events in the selected sequences were not detected using recombination detection program version 3.0 [55]. finally, we used tempest version 1.5.1 [56] to explore the presence of temporal structure in the sequence data and estimated a positive correlation […]

2017
PMCID: 5845698
PMID: 29168675
DOI: 10.1099/jgv.0.000963

[…] nos ky689676–ky689686 and mf120214–mf120224, respectively., blast was performed on the rvg gene segments, which indicated high nucleotide identity to human rvb vp6 and nsp3 gene segments. thus, rdp4 [31] was used to investigate potential recombination events between turkey rvg strains and human rvb strains. the sub-programmes geneconv, maxchi and chimaera in rdp4 detected potential […]

2017
PMCID: 5845698
PMID: 29168675
DOI: 10.1099/jgv.0.000963

[…] and nsp3 gene segments. thus, rdp4 [31] was used to investigate potential recombination events between turkey rvg strains and human rvb strains. the sub-programmes geneconv, maxchi and chimaera in rdp4 detected potential recombination in the vp6 gene segment, where the turkey rvg strains harboured a similar region in the 110–230 nucleotides to the human rvb/human-wt/ban/bang117/2002 (genbank […]

2017
PMCID: 5845698
PMID: 29168675
DOI: 10.1099/jgv.0.000963

[…] no. gu391305.1) fig. 1(a), which was visualized using a similarity plot with a two-parameter (kimura) distance model and a sliding window of 60 base pairs and step size of 10 base pairs. with rdp4, geneconv, bootscan, siscan and topal sub-programmes detected potential recombination between the turkey rvg strains, which harboured a similar region in the 130–270 nucleotides to the human […]

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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