The Editing & Color parameters control whether the assembly may be edited (and to what extent), as well as how different categories of bases are displayed in the Alignment View. Access these parameters by selecting Project > Parameters and Editing & Color from the list on the left.
From the Editing section, select from one of the following options:
Note: Editing selections are not applicable to BAM-based projects.
•All editing allowed enables you to perform all normal editing functions, including full use of the clipboard. Editing functions include addition and removal of gaps, and substitution of bases.
•Only gap editing allowed enables you to insert or delete sequence gaps. Changes to bases in the sequence are not allowed.
•No editing allowed disables all editing functions in the Alignment View.
The Colors section allows you to customize base colors in the Alignment View.
•Check Use consensus match color to distinguish Match and Mismatch colors. Click the box to the left of each word to open a color palette from which to choose the desired color.
•Check Use imported consensus color to distinguish the color of the bases used for the consensus in a Phrap assembly. Click the box to the left of Imported Consensus to open a palette from which to choose the desired color.
•Check Use other colors to distinguish bases that have had their weights negated. Click the box to the left of the Negated Weight and Trimmed options to choose each desired color.
•Check Use single letter protein codes if you prefer to view single letter codes in the Translation section of the Alignment View and for feature translations.