We present an update of the CLUMPY code for the calculation of the astrophysical J-factors (from dark matter annihilation/decay) for any Galactic or extragalactic dark matter halo including substructures: halo-to-halo concentration scatter may now be enabled, boost factors can include several levels of substructures, and triaxiality is a new option for dark matter haloes. This new version takes advantage of the cfitsio and HEALPix libraries to propose fits output maps using the HEALPix pixelisation scheme. Skymaps for γ-ray and ν signals from generic annihilation/decay spectra are now direct outputs of CLUMPY. Making use of HEALPix routines, smoothing by a user-defined instrumental Gaussian beam and computing the angular power spectrum of the maps are now possible. In addition to these improvements, the main novelty is the implementation of a Jeans analysis module, to obtain dark matter density profiles from kinematic data in relaxed spherical systems (e.g., dwarf spheroidal galaxies). The code is also interfaced with the GreAT toolkit designed for Markov Chain Monte Carlo analyses, from which probability density functions and credible intervals can be obtained for velocity dispersions, dark matter profiles, and J-factors. Program summaryProgram title:CLUMPYCatalogue identifier: AEKS_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKS_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 494335No. of bytes in distributed program, including test data, etc.: 24425968Distribution format: tar.gzProgramming language: C/C++.Computer: PC and Mac.Operating system: UNIX(Linux), MacOS X.RAM: Between 500MB and 1GB depending on the size of the requested skymapCatalogue identifier of previous version: AEKS_v1_0Journal reference of previous version: Comput. Phys. Comm. 183(2012)656Classification: 1.1, 1.7, 1.9.External routines: CERN ROOT (http://root.cern.ch), GSL (http://www.gnu.org/software/gsl), cfitsio (http://heasarc.gsfc.nasa.gov/fitsio/fitsio.html), HEALPix C++ and F90 (http://healpix.sourceforge.net/index.php), GreAT (http://lpsc.in2p3.fr/great) (for MCMC analyses only), and Doxygen (http://www.doxygen.org) (optional)Does the new version supersede the previous version?: YesNature of problem: Calculation of dark matter profile from kinematic data, γ-ray and ν signals from dark matter annihilation/decay.Solution method: Solve the integro-differential Jeans equation (optimised for speed) for several generic distributions (dark matter profile, light profile, velocity anisotropy). Integration of the DM density (squared) along a line-of-sight for generic dark matter haloes with substructures (spatial, mass, concentration distributions). Draw full skymaps of γ-ray and ν emission from dark matter structures, smoothed by an instrument PSF using HEALPix tools.Reasons for new version: Many more functionalities and options have been added to the code.Summary of revisions: Inclusion of the PPPC4DMID spectra for gamma-ray and neutrino fluxes; HEALPix pixelisation for skymaps and angular power spectrum; DM profile triaxiality enabled; More mass–concentration options; Multi-level substructure boost; Jeans analysis module to compute dark matter profiles for stellar kinematic data; Improved ROOT and FITS output.Restrictions: The diffuse extragalactic contribution to the signal (and γ-ray attenuation) as well as secondary radiation from dark matter remains to be included in order to provide a comprehensive description of the expected signal.Running time: This is highly dependent of the user-defined choices of DM profiles, precision ε and integration angle αint: •∼1 hour for a full skymap (including substructures) with αint=0.1° and ε=0.01;•∼=1 mn for a 5°×5° skymap (including substructures) with αint=0.1° and ε=0.01;•∼5 mn for a typical Jeans/MCMC analysis (on a ‘ultrafaint’-like dwarf spheroidal galaxy) using a constant anisotropy profile.