RDP4: Detection and analysis of recombination patterns in virus genomes

Abstract

RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of ‘recombination aware’ phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.

Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1

“…In this way, the deletion of repeat regions did not change the alignment of the genomes. These alignments, and the isolated UL, US or internal repeat regions, were then used to detect evidence of intraspecific recombination using two recombination detection programs: SplitsTree4 (Huson, 1998) and RDP4 (Martin et al, 2015). Initially, only the genomes of the Australian/New Zealand EHV isolates were analysed.…”

“…These methods were implemented in the program RDP4 (Martin et al, 2015). Analyses were performed using complete genome sequences, as well as alignments of the individual US, UL and IR regions.…”

New species in the papaya ringspot virus cluster: Insights into the evolution of the PRSV lineage

“…Identification of potential genome recombination sites was performed using RDP4 (Martin et al, 2015). This analysis sequentially tests every combination of three sequences in an input alignment for evidence that one of the three sequences is a recombinant and the other two are its parents.…”

Impact of Vat resistance in melon on viral epidemics and genetic structure of virus populations

“…The best substitution model was selected with MEGA. The absence of recombination signal in the different virus fragments analyzed was checked using 6 different recombination detection methods included in RDP4.0 (Martin et al, 2015). Distance and maximum-likelihood trees were built with MEGA using a bootstrap resampling (n= 500 bootstraps).…”