Suppose that the directory where the calculations are performed is /StructurePrediction. This directory will contain:
file INPUT.txt, thoroughly described in Section 4.
Subdirectory /StructurePrediction/Specific/ with VASP, SIESTA or GULP (etc.) executables, and enumerated input files for structure relaxation — INCAR_1, INCAR_2, …, and pseudopotentials.
Subdirectory /StructurePrediction/Seeds — contains files with seed structures and with a list of compositions/anti-compositions. Seed structures should be in VASP5 POSCAR format and concatenated in a file called POSCARS or POSCARS_gen (gen is the generation number). The compositions and Anti-compositions files are used to control the compositions during variable-composition or single-block calculations.
Subdirectory /StructurePrediction/AntiSeeds — you may put here particular structures that you wish to penalize, or use antiseed technique without specifying any structures explicitly (and penalize structures found during the run).