{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T04:26:54Z","timestamp":1776054414500,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2022,4,22]],"date-time":"2022-04-22T00:00:00Z","timestamp":1650585600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003150","name":"Fonds Qu\u00e9b\u00e9cois de la Recherche sur la Nature et les Technologies","doi-asserted-by":"publisher","award":["173878"],"award-info":[{"award-number":["173878"]}],"id":[{"id":"10.13039\/501100003150","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["249644"],"award-info":[{"award-number":["249644"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,26]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We have developed SimPlot++, an open-source multiplatform application implemented in Python, which can be used to produce publication quality sequence similarity plots using 63 nucleotide and 20 amino acid distance models, to detect intergenic and intragenic recombination events using \u03a6, Max-\u03c72, NSS or proportion tests, and to generate and analyze interactive sequence similarity networks. SimPlot++ supports multicore data processing and provides useful distance calculability diagnostics.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SimPlot++ is freely available on GitHub at: https:\/\/github.com\/Stephane-S\/Simplot_PlusPlus, as both an executable file (for Windows) and Python scripts (for Windows\/Linux\/MacOS).<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac287","type":"journal-article","created":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T03:15:01Z","timestamp":1650338101000},"page":"3118-3120","source":"Crossref","is-referenced-by-count":117,"title":["SimPlot++: a Python application for representing sequence similarity and detecting recombination"],"prefix":"10.1093","volume":"38","author":[{"given":"St\u00e9phane","family":"Samson","sequence":"first","affiliation":[{"name":"Department of Computer Sciences, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montreal, QC H3T 1N8, Canada"}]},{"given":"\u00c9tienne","family":"Lord","sequence":"additional","affiliation":[{"name":"Agriculture and Agri-Food Canada , Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3753-5925","authenticated-orcid":false,"given":"Vladimir","family":"Makarenkov","sequence":"additional","affiliation":[{"name":"Department of Computer Sciences, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al , Montreal, QC H3T 1N8, Canada"}]}],"member":"286","published-online":{"date-parts":[[2022,4,22]]},"reference":[{"key":"2023041403075715400_","doi-asserted-by":"crossref","first-page":"e4345","DOI":"10.1371\/journal.pone.0004345","article-title":"Using sequence similarity networks for visualization of relationships across diverse protein superfamilies","volume":"4","author":"Atkinson","year":"2009","journal-title":"PLoS One"},{"key":"2023041403075715400_","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1534\/genetics.105.048975","article-title":"A simple and robust statistical test for detecting the presence of recombination","volume":"172","author":"Bruen","year":"2006","journal-title":"Genetics"},{"key":"2023041403075715400_","doi-asserted-by":"crossref","first-page":"1964","DOI":"10.1093\/bioinformatics\/bth161","article-title":"GenAlyzer: interactive visualization of sequence similarities between entire genomes","volume":"20","author":"Choudhuri","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041403075715400_","doi-asserted-by":"crossref","first-page":"2620","DOI":"10.1093\/bioinformatics\/btq484","article-title":"Circoletto: visualizing sequence similarity with Circos","volume":"26","author":"Darzentas","year":"2010","journal-title":"Bioinformatics"},{"key":"2023041403075715400_","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1093\/bioinformatics\/bth500","article-title":"Recombination analysis tool (RAT): a program for the high-throughput detection of recombination","volume":"21","author":"Etherington","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041403075715400_","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. 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