DOTTER is a tool to render dot-matrix plots between nucleotide sequences, i.e., DNA and protein sequences. The main feature of DOTTER is that it allows the user to interactively adjust the alignment stringency using a 'Greyramp' tool.
E L Sonnhammer, R Durbin "A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis" Nat. Struct. Mol. Biol. 2009; 16(9):996-1001 https://doi.org/10.1016/0378-1119(95)00714-8
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