SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies

• Published in: BMC bioinformatics 2024-07, Vol.25 (1), p.235-13, Article 235
• Main Authors: Ouedraogo, Wend Yam D D, Ouangraoua, Aida
• Format: Article
• Language: English
• Subjects: Alternative splicing; Alternative Splicing - genetics; Analysis; Biological evolution; Branches; Care and treatment; Computer Simulation; Conserved sequence; Diagnosis; DNA sequencing; Environmental aspects; Evolution; Evolution, Molecular; Evolutionary biology; Evolutionary genetics; Exon-intron structure; Exons - genetics; Gene sequencing; Genes; Genetic aspects; Genetic disorders; Genetic engineering; Graphical user interface; Inference; Internet; Methods; Mutation; Nucleotide sequence; Phylogeny; Risk factors; Sequence analysis; Sequence Analysis, RNA - methods; Servers; Simulation; Software; Source code; Synthetic data; Transcript phylogeny
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05853-z

SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation. Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool. SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca , where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at  https://github.com/UdeS-CoBIUS/SimSpliceEvol .