I am not exactly sure what you mean by "software for cloning strategy",
but Gene Construction Kit, available from TextCo (www.textco.com) is a
very nice simulated cloning and plasmid viewing and editing program. It
keeps track of ends, will only allow things to insert correctly and you
can switch back and forth from sequence to graphic view. It is also
very good for producing figures. There is a free demo available at the
web site that will let you see the features of the program.
csgasser at ucdavis.edu