The Program I think you are asking about is SeqApp written by Don Gilbert.
This program is a freeware sequence editor that can do some basic and
useful things. The program can be found on the URL
1. You can perform multiple alignment by eye with the aid of colour fonts
in a multiple sequence editor window.
2. You can export sequences in various formats supported by what ever
alignment program that you use.
3. You can run CAP2 from the program. CAP2 will create a complete sequence
for you from your fragments.
Hope that this is of some help.
Dept. of Botany
e-mail: wikstrom at botan.su.se