I have a question regarding deletions in sequence alignments. Most alignment
programs use the formula ak+b to score an alignment of length k with b as the
fixed gap penalty and a as the incremental gap penalty. What are the default
values these parameters take in the common commercial alignment packages. Is
there a consensus about what these values should be or do people simply use
Thanks for any help people can give.
cohen at cumuli.vmsmail.ethz.ch