aop.sh is a shell wrapper script for the POA alignment program. It manages POA runs, automatically provides a scoring matrix, cleans FASTA files before and after the run, and computes pair-wise similarity scores with four different methods.
In order to run the script, you need to install POA (of course), bash, a modern awk (mawk or gawk) and for some of its functionality also sed (it works with GNU sed). These will be preinstalled on most UNIX/LINUX and MacOSX systems and can be used in conjunction with Cygwin under Windows.
If you use this script in a publication, please cite this web page.
In case you have any questions regarding this script, send an e-mail to support [AT] goeker [DOT] org. Please include "aop" somewhere in the subject.