Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. This sets the alternate display of matches and mismatches in alignments. Output file format The output from matcher is a sequence alignment. There are several ways to change the output format using -markx.
Users can provide their own data files in their own directories.
Warnings Diagnostic Error Messages Exit status 0 upon successful completion. Last modified 19th July 1999. This program is intended to be used by everyone and everything, from naive users to embedded scripts.