RDP4 specifications

Information


Unique identifier OMICS_13036
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

Taxon


  • Viruses

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Documentation


Maintainer


  • person_outline Darren P Martin <>

RDP4 articles

RDP4 citations

 (8)
2018
PMCID: 5831051

[…] 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 […]

2018
PMCID: 5794064

[…] to show the relationships among different sts or nsts and to visualize possible recombination events., the concatenated mlst and sbt sequences of our environmental isolates were screened using rdp4 to detect intragenic recombinations [33]. six methods implemented in the program rdp4 were utilized. these methods were rdp [34], geneconv, bootscan [35], maxchi [36], chimaera [37], and siscan […]

2015
PMCID: 4366220

[…] their in silico transcribed amino acid sequences were compared using blastn and blastp with genbank data. recombination analysis in the genomic sequences was performed using programs implemented in rdp4 [30]. mega5 [31] and splitstree 4 [32] were used for phylogenetic analysis and tree construction., purified camv (about 10 μg/ml) was applied to camv-free chlorella vulgaris (ccala ref. no: […]

2014
PMCID: 4183488

[…] file is available upon request. several recombination detection algorithms, such as rdp [40], geneconv [41], bootscan [42], maxchi [43], chimaera [44], siscan [45], and 3seq [46], all implemented in rdp4 beta 4.24 [47], were used to detect recombination among satbamv sequences. mega 5.2.1 [48] was used to estimate nucleotide diversity and conduct selection tests. to determine the standard error […]

2014
PMCID: 4086889

[…] (h5n1), and a/pintail duck/alberta/628/79 (h6n8), respectively., we screened homologous recombination in each gene segment of hpai h5n1 using various exploratory methods implemented in recombination detection program (rdp) version 4.22 [37], including rdp, geneconv and maxchi. sequences with mosaic recombination signals were identified as those with bonferroni-corrected p-values […]

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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