This paper presents the latest developments for the continuous-time system identification toolbox with fractional models (or fractional order systems): the CRONE toolbox. This toolbox is to be run with Matlab which includes time-domain identification algorithms for estimating continuous-time models directly from sampled data. The originality of the implemented algorithms is that they allow either fixing fractional differentiation orders or estimating them along with transfer function coefficients. One of the main issues when dealing with fractional models is their time-domain simulation. Three different time-domain simulation methods can be used independently from system identification methods. Output Error (OE), state variable filters (SVF) and (optimal) instrumental variables (IV) methods for ARX and OE models are provided to the end-user. The object oriented programming of the toolbox allows overloading standard script names. As a consequence, an end-user familiar with standard Matlab operators and scripts can use straightforwardly the CRONE toolbox.