Mutations are usually caused by errors in DNA replication. Nature frequently
deletes or inserts entire substrings as a unit, as opposed to deleting
or inserting individual nucleotides. A gap in an alignment is defined as a contiguous
sequence of spaces in one of the rows. Since insertions and deletions
of substrings are common evolutionary events, penalizing a gap of length x
as −x is cruel and unusual punishment. Many practical alignment algorithms
use a softer approach to gap penalties and penalize a gap of x spaces
by a function that grows slower than the sum of penalties for x indels.