ArticleBioinformatics advances2026
EvoSubster: a pipeline for evolutionary inference of single- and double-base substitution spectra.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Motivation: Mutational processes differ widely across the tree of life, yet most existing resources focus on somatic mutations in humans or on a limited set of well-studied species. Results: We present EvoSubster, a simple and extensible pipeline for inferring evolutionary single-base and double-base substitution spectra from closely related species using a parsimony-based three-genome comparison. The pipeline automatically downloads NCBI genomes, aligns them, infers substitution direction, quantifies single-base and double-base substitutions, and outputs visualizations. Applying EvoSubster to diverse fungal and cnidarian genomes revealed distinct lineage-specific substitutional signatures, including TTA>TCA and TTA>TGA in mushroom-forming fungi within Agaricomycetes, ACA>AAA and ACG>AAG in cnidarians, CG>TT and GC>AA in Mucoromycota, and frequent A: T-rich adjacent substitutions in Glomeromycetes (arbuscular mycorrhizal fungi). Availability and Implementation: EvoSubster is implemented as a set of Python 3, R, and bash scripts and is freely available on GitHub at: https://github.com/marikie/EvoSubster. The pipeline relies on a small number of easy-to-install, publicly available command-line tools. Installation instructions and example workflows are provided in the online documentation.
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