just have a look in your .gaprc file:
# which mode (1=by dots, 2=by fg color, 3=by bg color)
set_def CONTIG_EDITOR.DISAGREE_MODE 2
arnim wiezer <arnim at tower.goe.net> wrote in
news:Pine.LNX.4.44.0211050029320.4196-100000 at dna.g2l.bio.uni-goetting
> Hi !
>> I´m using gap4 4.6 (linux/alpha) and would like to ask if someone
> knows how to save the settings of the contig editor. Especially
> the Menu: Setting -> Highlight Disagreements -> by background
> color. It is quite boring to enable this button every time I open
> a new contig :-) I searched the documentation and the gaprc file,
> but didn´t find anything.
>> Any help appreciated :-)
>> best reagards,