Dot plots are a very simple method to visualize regions of similarity between two sequences. The sequences are placed on the horizontal and vertical axis, respectively. For each position in the diagram, a dot is drawn if the two characters in the sequences are identical at the corresponding positions. Adjacent regions of identity give rise to diagonal lines in the plot.

Dotlet [Junier et al. 2000] is a nice tool written in Java that generates dot plots for two given sequences.

Global (Needleman-Wunsch) alignments assume that two sequences are similar over their entire length. The alignment attempts to match the sequences from end to end, even if parts of them are not similar.

EMBOSS (European Molecular Biology Open Source Software Suite) [Rice et al. 2000] is a free open source software package for sequence analysis. It includes needle, a tool for global alignments.

Local (Smith-Waterman) alignments search for segments of two sequences that are similar. Only those parts of the sequences that have good matches according to some criterion are aligned.

water is the EMBOSS tool for local alignments.

Both EMBOSS tools needle and water can be used online at http://www.ebi.ac.uk/emboss/align/