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HREfinder / Homologous Recombination Events finder
Detects homologous recombination events from single-nucleotide polymorphism (SNP) data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. HREfinder is intended for hypothesis generation, and should be followed up by more detailed analyses of sequences, not just SNPs, to verify predicted HREs. HREfinder is intended to be used as a tool for hypothesis generation, so results are best interpreted and verified by more detailed analyses of the HRE predictions.
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