Emboss's Polydot: to create all-against-all dotplots of a set of sequences.
Emboss's Dottup: to create a wordmatch dotplot of two sequences.

In Polyplot, many sequences can be aligned to many others. If they are similar sequences, the dots align to form a diagonal line. In Dotplot, only two sequences can be aligned. Diagonal line represents regions of similarity. InDel's (insertions or deletions) are represented by breaks in the line. Word size affects both the plots in a similar manner. A very low word size increases the noise (many insignificant dots are seen) and thus effectively lowers the signal/noise ratio. A very high word size tends to decrease the effective signal along with the noise and thus affects the result. Thus, its important to keep a moderate word size so as to have the highest signal/noise ratio.