PAT is a Java-application for constructing multiple protein sequence alignments from regions of high similarity. It provides tools to identify, mark and align such regions. The sequences and the alignment can be visualized differently, e.g. using a special coloring of the amino acid symbols or displaying the sequences either as strings or schematically as rectangles. As the program is designed as a framework, it can be extended very easily. For example, you can implement and use additional algorithms for analyzing the sequences.
PAT is based on the program MACAW (Schuler GD, Altschul SF, Lipman DJ, 1991) and the implemented algorithm for searching local similarities, of which blocks can be constructed. In this way also protein sequences which share only a few domains can be compared. Global alignment algorithms would not be appropriate here.