RDP is a program for detecting recombination among aligned DNA sequences using a pairwise scanning approach. It runs on Windows95/98/NT and combines automated screening with an interactive graphical user interface. RDP analyzes multiple sequence alignments in various formats, examining every possible combination of three sequences for recombination evidence. It discards non-informative sites and identifies recombinant regions where sequence pairs show higher identity than the closely related pair. The probability of such a pattern occurring by chance is calculated using a binomial distribution. If this probability is below a user-defined threshold, the potential recombination is recorded. RDP's interface provides general and specific information about sequence relationships. While reference sequences are selected based on their positions in a UPGMA dendrogram, there may be cases where RDP cannot correctly distinguish between daughter and parental sequences. However, the program still approximates the correct recombination breakpoints. RDP has been used to analyze 86 full-length HIV and SIV genomes, identifying all previously known HIV-1 recombinants. It is available free of charge for academic use. RDP addresses the limitations of previous programs by offering an interactive interface and compatibility with common operating systems.RDP is a program for detecting recombination among aligned DNA sequences using a pairwise scanning approach. It runs on Windows95/98/NT and combines automated screening with an interactive graphical user interface. RDP analyzes multiple sequence alignments in various formats, examining every possible combination of three sequences for recombination evidence. It discards non-informative sites and identifies recombinant regions where sequence pairs show higher identity than the closely related pair. The probability of such a pattern occurring by chance is calculated using a binomial distribution. If this probability is below a user-defined threshold, the potential recombination is recorded. RDP's interface provides general and specific information about sequence relationships. While reference sequences are selected based on their positions in a UPGMA dendrogram, there may be cases where RDP cannot correctly distinguish between daughter and parental sequences. However, the program still approximates the correct recombination breakpoints. RDP has been used to analyze 86 full-length HIV and SIV genomes, identifying all previously known HIV-1 recombinants. It is available free of charge for academic use. RDP addresses the limitations of previous programs by offering an interactive interface and compatibility with common operating systems.