Figure 1

The AlignMiner algorithm. (A) Flow diagram of the main components of the algorithm, as explained in the text; the bold boxes are detalied in B. (B) The details of how a divergent region is obtained using a given scoring method. The "score calculation" renders a single numeric value for each MSA column. "FFT" is a fast Fourier transform for smoothing the curve of raw scores. The original (left branch) and Fourier-transformed (right branch) curves are trimmed with their respective "cutoffs" in order to obtain putative SNPs and conserved/divergent regions, respectively. The bold dashed boxes are detailed in C. (C) Details of the determination of the final cutoffs used for trimming scores and providing the validated conserved/divergent regions.