{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T18:38:37Z","timestamp":1771526317198,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2019\u201305058"],"award-info":[{"award-number":["RGPIN-2019\u201305058"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Gene duplication is a well-known driver of molecular evolution\u2014it acts as a source of genetic novelty, thereby providing the raw substrate for organismal adaption. However, detecting different types of gene duplicates and comparing them in sequence datasets can be difficult. Existing tools can identify and classify gene duplicates that have arisen by various processes, but have limitations; for example, some do not have a user-friendly workflow and can include many intermediate steps requiring manual adjustments of parameters and\/or are not maintained for the benefit of research community members. Here, we have developed HSDSnake, a user-friendly SnakeMake pipeline that can detect and classify gene duplications into five categories: dispersed, proximal, tandem, transposed, and whole genome. It also curates and evaluates the highly similar gene duplicates (HSDs) in each gene duplication category with reliance on both sequence similarity and conserved domains. Lastly, the detected gene duplicates can be visualized within a KEGG functional pathway framework and the substitution rates (Ka, Ks, and their Ka\/Ks ratio) can be analyzed for all the duplicate gene pairs. We demonstrate HSDSnake\u2019s capabilities by analyzing two reference genomes directly downloaded from NCBI and provide detailed instructions for each step.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The HSDSnake pipeline uses SnakeMake and Conda to run and install dependencies. The distribution version is available online at GitHub: https:\/\/github.com\/zx0223winner\/HSDSnake and the archived version at Zenodo is https:\/\/doi.org\/10.5281\/zenodo.15521945.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf325","type":"journal-article","created":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T16:43:26Z","timestamp":1748450606000},"source":"Crossref","is-referenced-by-count":2,"title":["HSDSnake: a user-friendly SnakeMake pipeline for analysis of duplicate genes in eukaryotic genomes"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2821-9066","authenticated-orcid":false,"given":"Xi","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Dalhousie University , Halifax, NS B3H 4R2,","place":["Canada"]},{"name":"Institute for Comparative Genomics, Dalhousie University , Halifax, NS B3H 4R2,","place":["Canada"]}]},{"given":"Yining","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Western University , London, ON N6A 5B7,","place":["Canada"]}]},{"given":"David Roy","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Biology, Western University , London, ON N6A 5B7,","place":["Canada"]}]},{"given":"Zhenyu","family":"Cheng","sequence":"additional","affiliation":[{"name":"Institute for Comparative Genomics, Dalhousie University , Halifax, NS B3H 4R2,","place":["Canada"]},{"name":"Department of Microbiology and Immunology, Dalhousie University , Halifax, NS B3H 4R2,","place":["Canada"]}]},{"given":"John M","family":"Archibald","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Dalhousie University , Halifax, NS B3H 4R2,","place":["Canada"]},{"name":"Institute for Comparative Genomics, Dalhousie University , Halifax, NS B3H 4R2,","place":["Canada"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,28]]},"reference":[{"key":"2025070408272022100_btaf325-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10539-018-9614-6","article-title":"The generality of constructive neutral evolution","volume":"33","author":"Brunet","year":"2018","journal-title":"Biol Philos"},{"key":"2025070408272022100_btaf325-B2","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2025070408272022100_btaf325-B3","doi-asserted-by":"crossref","first-page":"3378","DOI":"10.1093\/nar\/gkf449","article-title":"GenomeHistory: a software tool and its application to fully sequenced genomes","volume":"30","author":"Conant","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025070408272022100_btaf325-B4","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1007\/s00778-005-0153-9","article-title":"Rule-based workflow management for bioinformatics","volume":"14","author":"Conery","year":"2005","journal-title":"The VLDB J"},{"key":"2025070408272022100_btaf325-B5","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1111\/nph.15194","article-title":"Characterization of photosynthetic ferredoxin from the antarctic alga chlamydomonas sp. 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