Re-DOT-able requires two sequence files in order to draw a plot. Each file must be a DNA or RNA sequence file, in FastA format, which can potentially contain several sub-seqences. A so-called multi-fasta file.
A typical input sequence file for the program will look like this:
>seq1 this is the first sequence GAGGCTTATGCGGCTATGCGTAGTCGTAGTGCTAGTCGTAGCTAGCTAGTGCA ATATGCGTATTATATAAGGCGCGATATCGATCTGATGCTGTATGCTAGCGGTG AGGATCTGAGGAGAGGCGCGGATATATATGATGATGTGAGCGATGCGATGTGT >seq2 this is the second sequence ATATGCGTATTATATAAGGCGCGATATCGATCTGATGCTGTATGCTAGCGGTG AGGATCTGAGGAGAGGCGCGGATATATATGATGATGTGAGCGATGCGATGTGT >seq3 this is the third sequence GCTTATGCGGCTATGCGTAGTCGTAGTGCTAGTCGTAGCTAGCTAGTGCA
The main identifier for each sub-sequence will be the first set of non-whitespace text after the > sign. Any further text after that on the header line will be retained as the sequence description. The name for the sequence set as a whole will be taken from the filename from which the sequences were loaded.
You can have as many or as few sequences in each file as you like. The sequence can contain either N bases or ambiguity codes, but these will all be treated as mismatches when calculating alignments.
Before you can calculate an alignment you must have loaded a sequence file into both the x and y axes of the plot. If you want to compare a sequence against itself then simply load the same file twice.