## Draw dotplots for all-against-all comparison of a sequence set

### Description

This tool uses Emboss program ploydot to generate a dotplot for each of an all-against-all comparison of a set of sequences. The dotplots are rendered on a single diagram. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence searching for exact matches between sequence regions ("words"). The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a word from each sequences a dot is plotted. The wordsize is specified by the user. Optionally, information on the sequence and location of all the exact matching regions may be written to file as a feature file.

All sequence words of the specified size from the first input sequence are compared with all words from the second input sequence and exact matches identified. A line is plotted on the dotplot corresponding to any exact matching words. Thus any local regions of identity correspond to diagonals in the dotplot.

The input sequences can be in any of the EMBOSS compatible sequence formats. Note that this tool reads just one input file, that should contain all the sequences to be analyzed.

For more details, please check the manual page of polydot command.

### Output

Output is either an alignment report of sequence alignment file.