The Recombination Detection Program (RDP) is a software tool designed to detect recombination among aligned DNA sequences using a pairwise scanning approach. It runs on Windows95/98/NT and combines automated analysis with an interactive graphical user interface. RDP examines every possible combination of three sequences, discarding phylogenetically non-informative sites to create three information-rich sub-sequences. The software then calculates average percentage identities for each pair of sequences and identifies regions where sequences A and C or B and C are more closely related than sequences A and B. The probability of these relationships occurring by chance is estimated using the binomial distribution. If the probability is below a user-defined threshold, the potential recombination is stored for further analysis. RDP has been successfully used to analyze HIV and SIV genomes, identifying inter-subtype recombinants. The program's interface provides both general and specific information on the relationships between sequences, aiding in the interpretation of results.The Recombination Detection Program (RDP) is a software tool designed to detect recombination among aligned DNA sequences using a pairwise scanning approach. It runs on Windows95/98/NT and combines automated analysis with an interactive graphical user interface. RDP examines every possible combination of three sequences, discarding phylogenetically non-informative sites to create three information-rich sub-sequences. The software then calculates average percentage identities for each pair of sequences and identifies regions where sequences A and C or B and C are more closely related than sequences A and B. The probability of these relationships occurring by chance is estimated using the binomial distribution. If the probability is below a user-defined threshold, the potential recombination is stored for further analysis. RDP has been successfully used to analyze HIV and SIV genomes, identifying inter-subtype recombinants. The program's interface provides both general and specific information on the relationships between sequences, aiding in the interpretation of results.