At several points PAT provides the possibility to add additional functionality. These plug-ins consist of two types: The one bases on plain text files, the other on java implementations.
The text files affect the mtx-files of the score matrices and the col-files of the color schemes. The ones provided as default you can find in the directory files. You can open them in a normal text editor, modify them or add new ones. It is important that they are located in the default folders (matrices in files/matrix, color schemes in files/scheme) and that the defined format is kept, so that they can be read by the program.
With a little java knowledge you can add new algorithms to PAT. This concerns:
input- and output-parsers (current input: FASTA, GCG and NBRF, output: FASTA and GCG)
explorer-algorithms (currently MACAW, sequence-pattern-finder, repeat-finder)
conservation-scoring-algorithms (currently sum of pairs, weighted and unweighted entropy)
Here it is important that the classes belong to a certain package and implement a defined interfae. Furthermore, you must specify the path of these additional classes in the configuration file.
More information about the plug-ins you can find in the compositions.