Version 2.0 of CRPropa {[}CRPropa is published under the 3rd version of the GNU General Public License (GPLv3). It is available, together with a detailed documentation of the code, at https://crpropa.desy.de.] is public software to model the extra-galactic propagation of ultra-high energy nuclei of atomic number Z <= 26 through structured magnetic fields and ambient photon backgrounds taking into account all relevant particle interactions. CRPropa covers the energy range 7 x 10(16) < E/eV < A x 10(22) where A is the nuclear mass number. CRPropa can also be used to track secondary gamma-rays and neutrinos which allows the study of their link with the charged primary nuclei - the so called multi-messenger connection. After a general introduction we present several sample applications of current interest concerning the physics of extragalactic ultra-high energy radiation. (C) 2012 Elsevier B.V. All rights reserved.