RDP4 is an advanced software tool for detecting and analyzing recombination patterns in virus genomes. It is an updated version of the RDP program, capable of handling larger datasets (up to 2,500 sequences and 10Mb in length) and offering enhanced features such as differentiating between recombination and genome segment reassortment, estimating recombination breakpoint confidence intervals, and constructing phylogenetic trees with 'recombination-aware' methods. RDP4 can be run in automated mode or with a user-friendly interface for detailed exploration of individual and overall recombination patterns. The software provides tools for visualizing recombination hotspots, cold spots, and their impacts on phylogenetic trees, as well as testing the influence of various factors on recombination breakpoint patterns. It is designed to minimize the impact of recombination on phylogenetic analyses and can export alignments with recombinant sequences removed or split into their constituent parts. RDP4 is freely available for download and is suitable for both bacterial and viral genome datasets.RDP4 is an advanced software tool for detecting and analyzing recombination patterns in virus genomes. It is an updated version of the RDP program, capable of handling larger datasets (up to 2,500 sequences and 10Mb in length) and offering enhanced features such as differentiating between recombination and genome segment reassortment, estimating recombination breakpoint confidence intervals, and constructing phylogenetic trees with 'recombination-aware' methods. RDP4 can be run in automated mode or with a user-friendly interface for detailed exploration of individual and overall recombination patterns. The software provides tools for visualizing recombination hotspots, cold spots, and their impacts on phylogenetic trees, as well as testing the influence of various factors on recombination breakpoint patterns. It is designed to minimize the impact of recombination on phylogenetic analyses and can export alignments with recombinant sequences removed or split into their constituent parts. RDP4 is freely available for download and is suitable for both bacterial and viral genome datasets.