Palaeogeography is the study of the geography in the geological past, focusing on reconstructing the position of continents, oceans and mountain ranges over millions of years, helping scientists to understand past climates, the evolution of life and quantify sea-level variations. Plate tectonic models are essential for reconstructing palaeogeography, as they provide information about the position and age of geological features controlling the topography. The PANALESIS model, for instance, can be used to create fully quantified palaeogeographic reconstructions and sea-level variations estimates. However, the data and code used to produce previous results using PANALESIS were never published, were dependent on proprietary software, and can no longer be run due to software obsolescence, making them impossible to reproduce. To address this, we have entirely rewritten and enhanced the source code into a QGIS plugin named TopoChronia. In this paper, we present sea-level curves derived from the new palaeogeographic maps over the Phanerozoic, and compare them with the original PANALESIS sea-level curve as well as other data obtained with sequential stratigraphic studies. We discuss possible causes explaining differences in results. The TopoChronia plugin is available at https://github.com/florianfranz/topo_chronia