splitter is a simple editing program that allows you to split a long sequence into smaller, optionally overlapping, subsequences.
To split a sequence into subsequences of 10,000 bases (the default size) with no overlap between the subsequences:
% splitter one_huge.seq many_small.seq
To split a sequence into subsequences of 50,000 bases with an overlap of 3,000 bases on each subsequence:
% splitter one_huge.seq many_small.seq -size=50000 -over=3000