Pipeline to find recombinations using REDHORSE. REDHORSE accepts sorted alignments of “reads” to the genome (SAM/BAM) as input. REDHORSE extracts base composition at each genomic position from the BAM files using user defined parameters and compares this information with the reference genome to extract single nucleotide variations (SNVs). It consolidates the parental SNVs and retains markers where both parents are different while filtering out markers where both parents are same but different from the reference genome. It extracts the nucleotide information from all the samples at these marker positions and generates a “merged allele file” that includes physical genome positions and nucleotide information from each sample. And finally, it uses this “merged allele file” to extract CCs and DCs. It also converts the “merged allele file” to MSA format to be used as input to other RD algorithms. Optional filtering steps are not listed in this figure, see Methods.