The Options menu includes commands for adjusting global parameters for gap4. These include defaults to be used for dialogues and the cutoff values. The menu current contains two commands; Configure cutoffs and Select tags.
"Configure cutoffs" sets the default consensus and quality cutoff values and whether to treat sequence flagged with the Experiment File CH line) as double stranded. These parameters are used for all options computing the consensus. Using the CH line to represent double stranded data affects the quality calculations and hence which sections of the consensus sequence is to be considered as problematic or unfinished. For further details on the specific algorithms used and how these cutoff values relate see section The Consensus Calculation.
"Select tags" displays a window containing the known tag types. Each of these can be toggled by pressing the button next to the name. Several options have their own tag selection windows available (eg the Template Display and Assembly). These get their default set of active tags from those chosen using the Options menu, but once the option is started, any selections made are independent of those used elsewhere. For instance, setting the tags to display within the Template Display does not alter the default list of active tags when starting the Assembly option.