Figure 1

Method outline. Outline of the steps of the method, assuming 2 subtypes composed each of 2 sequences. The following color code for columns and nucleotides, respectively, is used in the topmost part: green - completely conserved columns (with respect to all subtype sequences and the query sequence), red - columns removed due to insertion by the query sequence or too much gaps in the alignment, yellow - minority nucleotides in the column. The part of the sequence coloured in gray (at the bottom) indicates a subtype yet unknown. The last row gives the classification of the query sequence into known and unknown positions.