C:\test>774383.pl
Gene1:Gene2 tags::
Group both under new tag: A

Gene3:Gene1 tags::A
Group first with second under A

Gene4:Gene1 tags::A
Group first with second under A

Gene2:Gene3 tags:A:A
Both grouped; add spcs

Gene2:Gene4 tags:A:A
Both grouped; add spcs

Gene3:Gene4 tags:A:A
Both grouped; add spcs

GeneA:GeneB tags::
Group both under new tag: B

GeneB:GeneC tags:B:
Group second with first under B

GeneC:GeneD tags:B:
Group second with first under B

GeneD:GeneE tags:B:
Group second with first under B

GeneE:GeneF tags:B:
Group second with first under B

GeneX:GeneY tags::
Group both under new tag: C

GeneX:GeneP tags:C:
Group second with first under C

{
  A => {
         genes => ["Gene1", "Gene2", "Gene3", "Gene4"],
         spcs  => [ 
             "spc1", "spc2", "spc1", "spc2", "spc4", "spc1", "spc2", "spc5", 
             "spc3", "spc1", "spc1", "spc2", "spc2", "spc3", "spc1", "spc2", 
         ],
       },
  B => {
         genes => ["GeneA", "GeneB", "GeneC", "GeneD", "GeneE", "GeneF"],
         spcs  => [ 
             "spc4", "spc5", "spc1", "spc2", "spc1", 
             "spc2", "spc4", "spc2", "spc3", "spc1", 
         ],
       },
  C => {
         genes => ["GeneX", "GeneY", "GeneP"],
         spcs  => ["spc6", "spc8", "spc6", "spc7"],
       },
}