Interpretation of cosmic-ray measurements on the ground or underground usually requires comparison with simulations of cosmic ray air-showers. Unfortunately, few of these simulation programs are found on the net.
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CORSIKA [COsmic Ray SImulations for KAscade] Air-shower simulation program (Karlsruhe, Germany)
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Electron Gamma Shower (EGS) web page at LBL (U.S.A.)
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Cosmos, GENAS, and EPICS simulation codes by K. Kasahara (Japan)
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AIRES [AIRshower Extended Simulations] at La Plata (Argentina)
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KASCADE simulation program (at DePauw university, U.S.A.) Link not operational.
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HEMAS-DPM air-shower simulation program by G. Battistoni, M. Carboni, and others. Link not operational.
Note: The KASCADE program above is not related to the KASCADE experiment.
Hadronic interaction models in air-shower simulation programs are usually based on programs developed for interactions at accelerator experiments, like NeXuS.
For a more extensive list of interaction simulation programs used in high-energy physics see here.
Simulation of the detector response to particles is frequently done with GEANT (which, occasionally, is also used for air-shower simulations).