The Options menu includes commands for adjusting global parameters for gap4. These currently include defaults to be used for dialogues, the cutoff values, and the general appearance of the application.
"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 are 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.
"Set maxseq" sets the maximum size of the consensus sequence within Gap4. This
includes concatenations consensus sequences (with extra space for text
headers). If an operation, such as assembly, requires using a sequence longer
than this amount then that operation will produce an error. This value can
also be adjusted by using the
-maxseq command line argument.See section Command Line Arguments.
"Set fonts" controls the fonts used for the various components of Gap4's windows. Be aware that some displays will not function correctly with any font. Examples are the contig editor, which requires a fixed space font. Similarly the main output window looks much better with a fixed space font. For more complete documentation, seesection Font Selection..
The "Colour" option sets the main colour scheme for Gap4 and other related programs. For more complete documentation, seesection Colour Selector..