I have an FastOrtho matrix, as follows:

ORTHOMCL0 (317 genes,19 taxa): PROKKA_01189(Firmino_Lb.brevis_3C0_TAAGGCGA-) PROKKA_02526(Firmino_Lb.brevis_3C0_TAAGGCGA-) ORTHOMCL1 (268 genes,19 taxa): PROKKA_02245(Firmino_Lb.brevis_3C0_TAAGGCGA-) PROKKA_00325(Firmino_Lb.brevis_3C0_TAAGGCGA-)

The order is: Ortholog group ID, Protein ID (e.g: Prokka_01189) and Strain ID( e.g: Lb_brevis_3C0...)

I need to make a matrix for presence and absence as the example below:

Ortho. group ID Strains Protein 1 Protein 2 Protein 100 MCL0 Lb brevis_3C0 1 0 0 MCL0 Lb brevis_3C7 1 1 1 MLC1 Lb brevis_3C0 0 0 0 MCL1 Lb brevis_3C7 1 1 1

Please, could someone help me? I really to get this done !!!!! Many thanks in advance

Fernanda