- Display help information
- Sort alignments by the query start coordinate
- Sort alignments by the reference start coordinate
- -w int
- Set the screen width - default is 60
- -x int
Set the matrix type - default is 2 (BLOSUM 62),
other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
note: only has effect on amino acid alignments
Input is the .delta output of either the "nucmer" or the "promer" program passed on the command line.
Output is to stdout, and consists of all the alignments between the query and reference sequences identified on the command line.
NOTE: No sorting is done by default, therefore the alignments will be ordered as found in the <deltafile> input.