badger requires a data file which contains the
genome arrangement sequences for at least two taxa. The format for the
file is a series of lines, one for each taxon. Each line consists of
the name of the taxon, followed by a comma, followed by a
comma-separated list of genes. Gene names may be integers or any
strings (not containing commas) and may be preceded by a minus sign
("-").
Here is an example of an input file:
CHOR Human,cox1,cox2,atp8,atp6,cox3,nad3,nad4L,nad4,nad5,-nad6,cob,rrnS,rrnL,nad1,nad2 CHOR Domestic Chicken,cox1,cox2,atp8,atp6,cox3,nad3,nad4L,nad4,nad5,cob,-nad6,rrnS,rrnL,nad1,nad2 HEMI Acornworm,cox1,cox2,atp8,atp6,cox3,nad3,nad4L,nad4,nad5,cob,-nad6,rrnS,rrnL,nad1,nad2 ECHI Sea star,cox1,nad4L,cox2,atp8,atp6,cox3,nad3,nad4,nad5,-nad6,cob,rrnS,-rrnL,-nad2,-nad1 ECHI Sea urchin,cox1,nad4L,cox2,atp8,atp6,cox3,nad3,nad4,nad5,-nad6,cob,rrnS,nad1,nad2,rrnL ECHI Crinoid,cox1,nad4L,cox2,atp8,atp6,cox3,nad3,nad4,nad5,-nad6,cob,-rrnS,-rrnL,-nad2,-nad1 BRACH Laqueus rubellus,cox1,cob,atp6,nad5,nad6,nad3,nad4L,cox3,atp8,nad2,cox2,rrnL,rrnS,nad1,nad4 BRACH T. transversa,cox1,cob,atp8,cox3,atp6,nad5,rrnS,nad6,rrnL,nad1,nad4,nad4L,cox2,nad3,nad2 BRACH T. retusa,cox1,cox2,atp8,atp6,rrnS,rrnL,nad1,nad6,cob,nad4L,nad4,nad5,cox3,nad3,nad2 ANNE Common earthworm,cox1,cox2,atp8,cox3,nad6,cob,atp6,nad5,nad4L,nad4,rrnS,rrnL,nad1,nad3,nad2 ARTH Cattle tick,cox1,cox2,atp8,atp6,cox3,nad3,-nad1,-rrnL,-rrnS,-nad5,-nad4,-nad4L,nad6,cob,nad2 ARTH Fruit fly,cox1,cox2,atp8,atp6,cox3,nad3,-nad5,-nad4,-nad4L,nad6,cob,-nad1,-rrnL,-rrnS,nad2 ARTH Hermit crab,cox1,cox2,nad3,nad2,atp8,atp6,cox3,-nad5,-nad4,-nad4L,nad6,cob,-nad1,-rrnL,-rrnS ARTH Wallaby louse,cox1,cox3,nad1,cob,-nad4,-nad4L,nad2,-nad5,cox2,-nad3,-rrnL,-rrnS,-atp6,-atp8,nad6 MOLL Squid,cox1,cox2,-nad5,-nad4,-nad4L,atp8,atp6,cox3,nad3,-cob,-nad6,-nad1,-rrnL,-rrnS,nad2 MOLL Black chiton,cox1,cox2,atp8,atp6,-nad5,-nad4,-nad4L,-cob,-nad6,-nad1,-rrnL,-rrnS,cox3,nad3,nad2 MOLL Land snail nemoralis,cox1,rrnL,nad6,nad5,nad1,nad4L,cob,cox2,-atp8,-atp6,-rrnS,-nad3,-cox3,nad4,nad2 MOLL Sea slug,cox1,rrnL,nad6,nad5,nad1,nad4L,cob,cox2,-atp8,-atp6,-rrnS,-nad3,nad4,-cox3,nad2 NEMA T. spirallis,cox1,cox2,nad1,-nad2,-nad5,-nad4,-nad4L,nad6,cob,rrnS,rrnL,atp6,cox3,atp8,nad3
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