{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T18:13:02Z","timestamp":1790273582909,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1014724","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000}}],"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004770","name":"Universit\u00e0 degli Studi di Parma","doi-asserted-by":"publisher","award":["FIL_2024_PROGETTI_B_BONNICI"],"award-info":[{"award-number":["FIL_2024_PROGETTI_B_BONNICI"]}],"id":[{"id":"10.13039\/501100004770","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an alignment-free and parameter-free approach based on k-mer profiles, combining high speed, ease of use, and competitive accuracy with state-of-the-art methods. However, the increasing availability of genomic data requires tools that can scale efficiently to larger datasets. To address this need, we present PanDelos-plus, a fully parallel, gene-centric redesign of PanDelos. The algorithm parallelizes the most computationally intensive phases (Best Hit detection and Bidirectional Best Hit extraction) through data decomposition and a thread pool strategy, while employing lightweight data structures to reduce memory usage. Benchmarks on synthetic datasets show that PanDelos-plus achieves up to 14x faster execution and reduces memory usage by up to 96%, while maintaining consistency with the original algorithm. These improvements allow the PanDelos methodology to be applied to population-scale comparative genomics, thus enabling more precise characterisation of pangenome structure and dynamics.<\/jats:p>\n                  <jats:p>\n                    PanDelos-plus is available at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/synbionics\/PanDelos-plus\" xlink:type=\"simple\">github.com\/synbionics\/PanDelos-plus<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1014724","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T17:45:42Z","timestamp":1789667142000},"page":"e1014724","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9596-0608","authenticated-orcid":true,"given":"Simone","family":"Colli","sequence":"first","affiliation":[{"name":"University of Parma","place":["Parma, Italy"],"department":["Department of Mathematical, Physical and Computer Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9885-6354","authenticated-orcid":true,"given":"Emiliano","family":"Maresi","sequence":"additional","affiliation":[{"name":"University of Parma","place":["Parma, Italy"],"department":["Department of Mathematical, Physical and Computer Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1637-7545","authenticated-orcid":true,"given":"Vincenzo","family":"Bonnici","sequence":"additional","affiliation":[{"name":"University of Parma","place":["Parma, Italy"],"department":["Department of Mathematical, Physical and Computer Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,17]]},"reference":[{"key":"pcbi.1014724.ref001","doi-asserted-by":"crossref","unstructured":"Yeh C-W, Huang C-W, Yang C-L, Wang Y-T. 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