Table 1.

Results for the Drosophila melanogaster use case

Assigned family	Reference family	Number of candidates
dmel_1	mdg3	12
dmel_3	opus	18
dmel_4	copia	24
dmel_5	springer	6
dmel_6	Burdock	16
dmel_7	diver	8
dmel_8	HMS-Beagle	10
dmel_9	Tirant	19
dmel_10	Tabor	4
dmel_11	Quasimodo	14
dmel_12	Transpac	9
dmel_14	flea	16
dmel_17	invader2	8
dmel_17_2	invader3	7
dmel_18	Max-element	4
dmel_22	3S18	6
dmel_24	McClintock	4
dmel_26	Stalker	25
dmel_32	17.6	18
dmel_33	412	17
dmel_34	412	9
dmel_36	Idefix	5
dmel_39	rover	5
dmel_46	micropia	3
newfam_0	blood	25
newfam_29	HMS-Beagle2	4
newfam_40	297	20
manual	gypsy4	7
manual	mdg1	17
manual	roo	94

This table lists the putative families as assigned during our semi-automatic evaluation run on the Drosophila melanogaster genome (left column). The center column shows the name of the known family represented by that putative family, obtained from matching of the candidate sequence against a reference sequence set. The rightmost column lists the number of candidates in the respective family. The dmel_26 group (matched to various Stalker sequences) was not counted as recovered due to the multitude of non-unique matches to multiple references. Families with the newfam prefix were obtained by re-running the classification algorithm on subsets of the unclassified candidate set. Finally, families marked as manual were derived non-automatically.