We describe techniques for comparing spectra extracted from cosmological simulations and observational data, using the same methodology to link Lyα properties derived from the simulations with properties derived from observational data. The eventual goal is to measure the coherence or clustering properties of Lyα absorbers using observations of quasar pairs and groups. We quantify the systematic underestimate in opacity that is inherent in the continuum-fitting process of observed spectra over a range of resolution and signal-to-noise ratio (S/N). We present an automated process for detecting and selecting absorption features over the range of resolution and S/N of typical observational data on the Lyα forest. Using these techniques, we detect coherence over transverse scales out to 500 h kpc in spectra extracted from a cosmological simulation at z = 2.