VisRD

VisRD detects recombination events and identifies recombination breakpoints in sequence alignments by applying quartet-mapping to analyze phylogenetic content.

Key Features:

• Quartet-mapping based recombination detection: Applies quartet-mapping to sequence alignments to identify recombinant sequences and breakpoints without requiring predefined query or reference sequences.
• Evaluation of identification statistics and tests: Assesses different recombinant identification statistics and significance tests through simulations.
• Comparison with triplet-based methods: Compares quartet scanning with triplet-based methods that use heuristic tests for identifying parental and recombinant sequences, showing relatively good performance for identifying descendants of older recombination events in simulations.
• Graphical inspection of alignments: Produces graphical representations of sequence alignments to reveal phylogenetic anomalies indicative of recombination.

Scientific Applications:

• Viral evolution studies: Characterizes recombination patterns in molecular sequences to inform analyses of viral evolutionary dynamics.
• HIV-1 and SIV analysis: Applied to well-established and putative HIV-1 recombinant strains, providing evidence relevant to the lineage status of CRF02_AG and the recombinant origin of subtype G, confirming intrasubtype recombination in HIV-1, and disentangling recombinant histories of SIV lineages.

Methodology:

Scans sequence alignments using a quartet-mapping strategy without predefined query/reference sequences, evaluates recombinant-identification statistics and significance tests via simulations, and compares results to triplet-based methods that incorporate heuristic tests for parental and recombinant sequence identification.