- +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"\r
- +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"\r
+ +"-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