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The alignments to the genome from next-generation-sequencing (NGS) data cannot be directly used as input to the existing recombination detection (RD) algorithms that use multiple sequence alignments (MSA). We therefore designed a software suite called REDHORSE that takes genomic alignments as input, extracts meaningful markers and generates MSAs that are the inputs to existing RD algorithms. In addition, REDHORSE implements a custom RD algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is portable and platform independent suite that provides efficient analysis of genetic crosses based on NGS data.
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