I want to store all sequence traces of a sequencing project (using Staden) in one file. You can do that if you simply tar all the *.ztr files: tar -cvf ./test.tar *.ztr Then you have to specify in gap4 Options -> Configure menus -> Expert And then you need to specify Options -> Trace file location -> TAR=./test.tar
To make one sequence a reference sequence, just select its name from the gap4 Edit Contig window and right click and select as reference sequence. If the file is in embl format, the features will show up as Staden tags in the alignment.
Today I installed the Staden Package on Tanja's Macintosh G4 computer (MacOS 10.3). I recommend using the ebiotools package made by Anders Nister. It includes other useful software such as EMBOSS, Blast, etc.). Installation instructions are available in the embnet news issues 9/1, 9/2, 9/3 and 10/1 or gathered into one pdf file from here.