Abstract
Summary 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).
Availability and Implementation The workflow is available for Linux, written as a Nextflow workflow which calls established genomics and phylogenetics tools to streamline the analysis and visualisation of genome divergence. This workflow is freely available at https://github.com/jeffersonfparil/compare_genomes, distributed under the GNU General Public License version 3 (GPLv3).
Contact Corresponding author: Jeff Paril jeff.paril{at}unimelb.edu.au. Queries and issues regarding the implementation can be submitted on the issue page of the github repository: https://github.com/jeffersonfparil/compare_genomes/issues.
Competing Interest Statement
The authors have declared no competing interest.