DOI: 10.1101/2023.03.16.533049

compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes

J.Paril T. Zare A. Fournier-Level

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The dawn of cost-effective genome assembly is enabling deep comparative genomics to address fundamental evolutionary questions by comparing the genomes of multiple species. However, comparative genomics analyses often deploy multiple, often purpose-built frameworks, limiting their transferability and replicability. Here, we developed compare_genomes, a transferable and extensible comparative genomics workflow package which streamlines the identification of orthologous families within and across genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein-coding sequences).

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