RDP5

RDP5 detects and characterizes recombination events within nucleotide sequence datasets to support molecular evolution and phylogenetic analyses.

Key Features:

• Recombination detection: Automatically detects and characterizes recombination events in nucleotide sequence alignments.
• Statistical testing: Incorporates statistical tests to distinguish true recombination signals from those potentially arising from other evolutionary processes.
• Scalability: Processes alignments containing up to 5,000 sequences with sequence lengths up to 50 million sites.
• Performance: Implements algorithmic enhancements delivering up to fivefold speed increases relative to RDP4.
• Recombinant disassembly: Disassembles recombinant sequences into inferred parental components and produces recombination-free datasets in multiple alignment formats.
• Manual verification and data management: Provides tools for manual verification of detected recombination events along with data management and visualization functions.

Scientific Applications:

• Phylogenetic analysis: Identify and remove recombination signals to improve phylogenetic inference.
• Molecular evolution: Generate recombination-free datasets for molecular evolution and comparative sequence analyses.
• Recombination history exploration: Investigate and reconstruct recombination histories within nucleotide datasets.

Methodology:

Automated recombination detection using incorporated statistical tests to distinguish true recombination signals, algorithmic enhancements for increased processing speed, and disassembly of recombinant sequences into original components.