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From the help page "Changing the contig order": "The contig order is saved automatically whenever a contig is created or removed (eg auto assemble), including operations like disassemble which temporarily create contigs. The order can be saved manually using the Save Contig Order option on the File menu."
I can not find the Save Contig Order option neither in the main File menu of gap4 nor in the File menu from the contig selector window. How can I save my contig order?
It's in the main Edit menu, or at least it is if you declare yourself to be an expert. Most of these esoteric features are hidden from novice users so as not to overwhelm people with zillions of (sometimes fairly useless!) functions. See the main Options menu to enable this.