Gap4 can label segments of readings and contigs using "tags" (see section Create Tag). The program recognises a set of standard tags types and users can also invent their own. Each tag type has a unique four character identifier, a name, a direction, a colour and a text string for recording notes. Tags can be created, edited and removed by users and by internal routines. Tags can also be input along with readings. This is important when reference sequences are used during mutation detection (see section Reference sequences).