- +"-groups FILE\tUse the given file to mark groups on the alignment."\r
- +"\nThe first lines of the groups file lists the GroupName and GroupColours"\r
- +" to be used in the alignment. Use the GROUPNAME label for each of your sequences. "\r
- +"\nGROUPNAME<tab>GROUPCOLOUR\n"\r
- +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>GROUPNAME\n"\r
- +"SequenceID is used in preference to SequenceIndex if both are provided.\n"\r
- +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"\r
- +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"\r
+ +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"\r
+ +"-features FILE\tUse the given file to mark features on the alignment.\n"\r