RDP3 is an advanced version of the RDP program designed for analyzing recombination events in DNA sequence alignments. It introduces several new methods for recombination detection, including 3SEQ, VISRD, PHYLRO, and LDHAT, as well as new tests for recombination hotspots. The program offers a range of visualization tools and recombination-aware ancestral sequence reconstruction methods. RDP3 is highly automated and user-friendly, with an interactive graphical interface that allows for detailed cross-checking of results. It can handle large datasets, analyzing alignments from 1000 × 10 kilobase to 20 × 2 megabase sequences within 48 hours on a desktop PC. The program is freely available from its website and includes a comprehensive manual with detailed descriptions and usage guidelines.RDP3 is an advanced version of the RDP program designed for analyzing recombination events in DNA sequence alignments. It introduces several new methods for recombination detection, including 3SEQ, VISRD, PHYLRO, and LDHAT, as well as new tests for recombination hotspots. The program offers a range of visualization tools and recombination-aware ancestral sequence reconstruction methods. RDP3 is highly automated and user-friendly, with an interactive graphical interface that allows for detailed cross-checking of results. It can handle large datasets, analyzing alignments from 1000 × 10 kilobase to 20 × 2 megabase sequences within 48 hours on a desktop PC. The program is freely available from its website and includes a comprehensive manual with detailed descriptions and usage guidelines.