Jones, J.K. Thompson, N. JACoW Geneva, Switzerland 978-3-95450-182-3 10.18429/JACoW-IPAC2017-TUPIK108 English 1971-1974 TUPIK108 FEL quadrupole alignment undulator cavity Contribution to a conference proceedings 2017 2017-05 http://dx.doi.org/10.18429/JACoW-IPAC2017-TUPIK108 http://jacow.org/ipac2017/papers/tupik108.pdf The CLARA (Compact Linear Accelerator for Research and Applications) test facility is designed to experimentally demonstrate innovative FEL schemes for future light source applications. Such schemes can place strict requirements on the accelerator beam properties as well as the relative alignment of the beam in the FEL radiators and modulators. Beam-based alignment (BBA) of the FEL section is therefore an operational requirement for all advanced FEL facilities. In this paper we demonstrate results of CLARA BBA simulations, and also report initial simulation results from the use of non-linear algorithms to optimise the FEL performance directly.