I have used Sequencher, at several different places with very different
projects. This program is very useful, simple-to-use, and
well-supported. Being Mac-based and networked, it is especially useful
for institutions that do not have a dedicated computer support staff.
For ex., in a pharmaceutical setting, over seventy-five different
researchers, with different needs and backgrounds, were able to use
Sequencher to analyze DNA sequences retrieved form a core facility (with
little training). I've used this program to assemble cosmid-, plasmid-,
and gene-sized projects, as well as to align few sequences. Again,
GeneCodes is very receptive to suggestions and will respond to questions
and problems.