The present paper addresses topics from various fields of biology. Its purpose is to enlarge the understanding of the usage of bioinformatics tools in the phylogenetic analysis of RNA viruses. The paper highlights the benefits of using information technology in virology, bringing the scientific community closer to unraveling the mysteries of RNA virus evolution and their adaptation to different niches and hosts and facilitating the understanding of their rapid mutation processes. Phylogenetic analysis of genetic sequences allows the exploration of the causes of these genetic changes in viruses and categorizes them into taxonomic groups. This paper is a systematic review of the most important scientific articles on the phylogenetic analysis of RNA viruses using bioinformatics. The studies included in the review were selected based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines and discuss methods for analyzing genetic and protein sequences (including codon sequences) and describe phylogenetic analyses and the bioinformatics tools used (such as VConTACT, RAxML, etc.). This review emphasizes the importance of further development in the fields of bioinformatics and virology, particularly with respect to RNA viruses, in order to mitigate the risk of a future pandemic. It also aims to provide a detailed understanding of the mutation and evolution mechanisms of these entities, which will help in efforts to limit viral virulence, for example. This article did not receive any funding for its creation and has not been registered in any database.