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RDP4 specifications


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
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




No version available



  • person_outline Darren P Martin

Publications for Recombination Detection Program

RDP4 citations


Characterization of a new apple luteovirus identified by high throughput sequencing

Virol J
PMCID: 5952423
PMID: 29764461
DOI: 10.1186/s12985-018-0998-3

[…] of the P1-P2 and CP aa sequences were analyzed but close relationship of the four viruses were retained (data not shown). Analysis of the genomic sequences of 45 species of the family Luteoviridae by RDP4 did not detect any recombination breakpoints.Fig. 3 […]


Tracking HIV 1 recombination to resolve its contribution to HIV 1 evolution in natural infection

Nat Commun
PMCID: 5954121
PMID: 29765018
DOI: 10.1038/s41467-018-04217-5

[…] infected individuals. RAPR classifies sequences depending on whether they originated from the T/Fs via mutation or from a recombination event between T/F lineages. Compared to existing programs like RDP4 and GARD, our simple simulations indicate that RAPR is more sensitive in detecting recombination events particularly in low-diversity settings (e.g., about 1%). RAPR has a built-in mechanism to c […]


Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Sci Rep
PMCID: 5951951
PMID: 29760429
DOI: 10.1038/s41598-018-25936-1
call_split See protocol

[…] es were calculated using Maximum Composite Likelihood model. The evolutionary analyses were conducted in MEGA 7. In order to identify the possibly recombinant origin(s) of CanineCV TH/2016 strains, a recombination detection program 4 (RDP4) package v. Beta 4.94, an integrated software program was used. Briefly, the recombination events of CanineCV’s TH/2016 were detected by using a range of recomb […]


Characterization of the first complete genome sequence of an Impatiens necrotic spot orthotospovirus isolate from the USA and worldwide phylogenetic analyses of INSV isolates

BMC Res Notes
PMCID: 5946465
PMID: 29747679
DOI: 10.1186/s13104-018-3395-5
call_split See protocol

[…] eplicates. 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. […]


Polymorphism in merozoite surface protein 7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure

PLoS One
PMCID: 5931635
PMID: 29718980
DOI: 10.1371/journal.pone.0196765

[…] ties were inferred for categories 6–8 with their relative percent probability set at 99.9% []. Evidences of genetic recombination were analyzed by using the Recombination Detection Program version 4 (RDP4) that includes RDP4, GENCONV, Bootscanning, the Maximum Chi Square, CHIMAERA, Sister Scanning and 3SEQ methods []. The fixation index (Fst) was deployed to evaluate the level of population differ […]


A traditional evolutionary history of foot and mouth disease viruses in Southeast Asia challenged by analyses of non structural protein coding sequences

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

[…] (KY322676) 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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