The software of the geographical information system for studying the Earth's natural disasters (GIS-ENDDB) is focused on the research into cause-and-effect relations of catastrophic events in our planet's history. It contains data on the Earth's seismic activity, anomalies of heat flows (HF), gravitational field and tomography layers, detailed geographical relief, as well as data on cosmogenic structures distribution. To develop methods for analyzing these data, it has been added into the subsystems of information and mathematical software updates such as: the algorithm for building seismicity lineaments in terms of the Great circles (GC) of the Earth; the algorithms for constructing the contours of a maximum earthquake magnitudes and of the averaging earthquake mechanisms; the functions of geophysical fields visualization and the cross-section visualization of different seismicity characteristics; and tomography data. All these updates help to extend the capabilities of classical methods for geotectonic studies by a complex scientific-experimental approach allowing one to reveal tectonically active faults, to study the spatial relationship of seismicity and cosmogenic paleostructures (related to the historical past of the Earth), and, eventually, to interpret the data in terms of constructing seismic-geodynamic models of the lithosphere.