The Persephone data structure allows grouping similar tracks under a track tree node, thus forming a hierarchical structure of track nodes. Following this logic, when adding a track tree node, PersephoneShell will first ask which tracks will be grouped and then will ask to name the new group.

To add a track tree node enter 'add tracktreenode' followed by the Map Set (in a form of id or path). Unlike adding the real track data, when you add a track tree node, PersephoneShell displays a menu instead of performing the addition immediately. The following shows an example of adding a track tree called "Other gene models" that combines Tracks 2,3 and 12 for a map set with the MapSet identified by map set path.

PS> add tracktreenode "Arabidopsis thaliana/Arabidopsis annotation v. 10"
TrackTree for MapSet 'Arabidopsis annotation v. 10':
[0] GENBANK (CDS) (Track, Order: 0, Type: Annotation)
[1] MRNA (Track, Order: 1, Type: Annotation)
[2] FGENESH (CDS) (Track, Order: 2, Type: Annotation)
[3] GlimmerHMM (CDS) (Track, Order: 4, Type: Annotation)
[4] Blast Tracks (Group, Order: 16)
 [5] PLANT_NR_HITS (Track, Order: 12, Type: Alignment)
 [6] blast vs plant_nr (Track, Order: 14, Type: Alignment)
 [7] plant nr tblastn (Track, Order: 15, Type: Alignment)
 [8] plant_nr partitioned (Track, Order: 16, Type: Alignment)
 [9] plant nr partitioned 3 (Track, Order: 17, Type: Alignment)
[10] Bedgraph Tracks (Group, Order: 17)
 [11] Large Bedgraph Tracks (Group, Order: 17)
  -- no items --
[12] FGENESH2 (CDS) (Track, Order: 20, Type: Annotation)
[13] Structural Variations (Track, Order: 27, Type: GenericBp)
[14] Ceres (Group, Order: 30)
 [15] Ceres_Leads (Track, Order: 28, Type: GenericBp)
 [16] Ceres Clones (Track, Order: 29, Type: Annotation)
Enter one or more [NodeNumber] to group (separated by comma)? 2,3,12
New NodeName? Other gene models
Parent [NodeNumber]?
Order No? 3
Do you really want to ADD the GroupNode? (Y/N) Y