Influenza virus is one of the most rapidly evolving human pathogens and causes significant morbidity and mortality worldwide. This feature enables the virus to avoid natural or vaccine-induced immunity. For this reason, there is an intensive search for new approaches to create a universal influenza vaccine. Here, we propose pipelines based on modern prediction algorithms that allowed us to select 10 B-cell epitopes, 10 CD8+ T-cell epitopes and 6 CD4+ T-cell epitopes from influenza viruses that were characterized by high conservation and antigenicity. These epitopes could be used to create universal vaccines against influenza viruses. In addition, the scripts used in these pipelines are universal and can be used to select epitopes from other pathogens.