RDP4

RDP4 is a Windows-based desktop application for detecting and analyzing recombination in aligned nucleotide sequence datasets. Widely used in molecular evolution and virology research, it integrates multiple complementary statistical methods to scan for recombination signals, pinpoint breakpoints, and infer likely parental lineages. The software provides interactive visualizations and detailed reports to help researchers validate findings and curate alignments prior to downstream phylogenetic or selection analyses.

Key features:

• Combines several established detection methods (e.g., RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, 3Seq) to increase confidence through consensus calling
• Maps recombination breakpoints and suggests putative major and minor parents
• Offers interactive plots and evidence summaries to inspect signals and reduce false positives
• Supports analysis of aligned nucleotide sequences (e.g., FASTA) with adjustable significance thresholds and multiple-testing controls
• Exports results and summaries for reproducibility and reporting

Notes:

• Accuracy depends on alignment quality and appropriate sequence diversity
• Cross-validation with multiple methods and careful parameter tuning is recommended
• Although built for Windows, it may run on other operating systems via compatibility layers such as Wine

RDP4 is developed by University of Cape Town. The most popular version of this product among our users is 4.1. The names of program executable files are RDP4.exe, RDP5.exe.