Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks ( https://github.com/biocorecrg/ExOrthist ).

Centre for Genomic Regulation Barcelona Institute of Science and Technology Dr Aiguader 88 08003 Barcelona Spain

Department of Zoology Charles University Vinicna 7 12844 Prague Czech Republic

ICREA Barcelona Spain

San Francisco State University 1600 Holloway Ave San Francisco CA 94132 USA

Universitat Pompeu Fabra Barcelona Spain

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ExOrthist: a tool to infer exon orthologies at any evolutionary distance