{"id":"https://openalex.org/W2891714529","doi":"https://doi.org/10.1093/bioinformatics/bty594","title":"S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks","display_name":"S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks","publication_year":2018,"publication_date":"2018-07-06","ids":{"openalex":"https://openalex.org/W2891714529","doi":"https://doi.org/10.1093/bioinformatics/bty594","mag":"2891714529","pmid":"https://pubmed.ncbi.nlm.nih.gov/30423060"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty594","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty594","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i680/25702223/bty594.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i680/25702223/bty594.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113980524","display_name":"Hongwei Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hongwei Yan","raw_affiliation_strings":["Department of Mathematics, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069875593","display_name":"Andreas D. M. Gunawan","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Andreas D M Gunawan","raw_affiliation_strings":["Department of Mathematics, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012300835","display_name":"Louxin Zhang","orcid":"https://orcid.org/0000-0003-0260-824X"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Louxin Zhang","raw_affiliation_strings":["Computational Biology Program, National University of Singapore, Singapore","Department of Mathematics, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Program, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Mathematics, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012300835"],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2079,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.81579136,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"34","issue":"17","first_page":"i680","last_page":"i686"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8479999899864197,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8479999899864197,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.1412999927997589,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12090","display_name":"Language and cultural evolution","score":0.001500000013038516,"subfield":{"id":"https://openalex.org/subfields/3316","display_name":"Cultural Studies"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8916810750961304},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6378916501998901},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.632976770401001},{"id":"https://openalex.org/keywords/extant-taxon","display_name":"Extant taxon","score":0.5904309749603271},{"id":"https://openalex.org/keywords/reticulate","display_name":"Reticulate","score":0.5388922095298767},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.487308144569397},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4849562644958496},{"id":"https://openalex.org/keywords/containment","display_name":"Containment (computer programming)","score":0.4808843433856964},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.420653760433197},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4169083833694458},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3821146488189697},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3178568482398987},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2293069064617157},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.2066100537776947},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17951452732086182}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8916810750961304},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6378916501998901},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.632976770401001},{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.5904309749603271},{"id":"https://openalex.org/C2780432395","wikidata":"https://www.wikidata.org/wiki/Q21149008","display_name":"Reticulate","level":2,"score":0.5388922095298767},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.487308144569397},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4849562644958496},{"id":"https://openalex.org/C2777019822","wikidata":"https://www.wikidata.org/wiki/Q390066","display_name":"Containment (computer programming)","level":2,"score":0.4808843433856964},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.420653760433197},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4169083833694458},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3821146488189697},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3178568482398987},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2293069064617157},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2066100537776947},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17951452732086182},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty594","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty594","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i680/25702223/bty594.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30423060","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30423060","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/156494","is_oa":false,"landing_page_url":"https://scholarbank.nus.edu.sg/handle/10635/156494","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Elements","raw_type":"Conference Paper"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty594","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty594","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i680/25702223/bty594.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G778910513","display_name":null,"funder_award_id":"NRF2016NRF-NSFC001-026","funder_id":"https://openalex.org/F4320321038","funder_display_name":"Fonds National de la Recherche Luxembourg"}],"funders":[{"id":"https://openalex.org/F4320321038","display_name":"Fonds National de la Recherche Luxembourg","ror":"https://ror.org/039z13y21"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1597020313","https://openalex.org/W1772827403","https://openalex.org/W1808849622","https://openalex.org/W1997224462","https://openalex.org/W2005892692","https://openalex.org/W2022927779","https://openalex.org/W2052184658","https://openalex.org/W2054547415","https://openalex.org/W2062962705","https://openalex.org/W2099352568","https://openalex.org/W2107385756","https://openalex.org/W2109419864","https://openalex.org/W2112400707","https://openalex.org/W2117665706","https://openalex.org/W2131783665","https://openalex.org/W2141282191","https://openalex.org/W2143424400","https://openalex.org/W2168704151","https://openalex.org/W2168907268","https://openalex.org/W2484986946","https://openalex.org/W2496112388","https://openalex.org/W2530251111","https://openalex.org/W2560525892","https://openalex.org/W2597162109","https://openalex.org/W2914729178","https://openalex.org/W3098329170","https://openalex.org/W4236590756","https://openalex.org/W4243187486","https://openalex.org/W6684836360"],"related_works":["https://openalex.org/W2007492229","https://openalex.org/W2365588293","https://openalex.org/W4387455607","https://openalex.org/W2055298722","https://openalex.org/W2135713257","https://openalex.org/W2104287568","https://openalex.org/W4362657803","https://openalex.org/W4305020964","https://openalex.org/W2951456975","https://openalex.org/W3144097773"],"abstract_inverted_index":{"Motivation:":[0],"Comparative":[1],"genomic":[2,25],"studies":[3],"indicate":[4],"that":[5],"extant":[6],"genomes":[7],"are":[8,72,144],"more":[9],"properly":[10],"considered":[11],"to":[12,39,47,83,100,128,200],"be":[13],"a":[14,88,94,103,109,116,135,151,175,190],"fusion":[15],"product":[16],"of":[17,30,58,69,105,189,197],"random":[18],"mutations":[19],"over":[20],"generations":[21],"(vertical":[22],"evolution)":[23],"and":[24,43,61,75,142,205],"material":[26],"transfers":[27],"between":[28],"individuals":[29],"different":[31],"lineages":[32],"(reticulate":[33],"transfer).":[34],"This":[35,182],"has":[36,155],"motivated":[37],"biologists":[38],"use":[40],"phylogenetic":[41,59,70,89,95,117,167],"networks":[42,60,71],"other":[44],"general":[45],"models":[46],"study":[48],"genome":[49],"evolution.":[50],"Two":[51],"fundamental":[52],"algorithmic":[53],"problems":[54],"arising":[55],"from":[56,62,193],"verification":[57],"computing":[63],"Robinson-Foulds":[64],"distance":[65],"in":[66,93,111,115,159],"the":[67,73,130,139,147,180,187,194,198,201],"space":[68],"tree":[74,90,113,140],"cluster":[76,110,120],"containment":[77,121,141],"problems.":[78],"The":[79,97,119,207],"former":[80],"asks":[81],"how":[82],"decide":[84,101],"whether":[85,102],"or":[86],"not":[87],"is":[91,99,124,184,210],"displayed":[92,114],"network.":[96,118,137],"latter":[98],"subset":[104],"taxa":[106],"appears":[107],"as":[108],"some":[112],"problem":[122],"(CCP)":[123],"also":[125],"closely":[126],"related":[127],"testing":[129],"infinite":[131],"site":[132],"model":[133],"on":[134,165,186,214],"recombination":[136],"Both":[138],"CCP":[143,148,199],"NP-complete.":[145],"Although":[146],"was":[149],"introduced":[150],"decade":[152],"ago,":[153],"there":[154],"been":[156],"little":[157],"progress":[158],"developing":[160],"fast":[161,176],"algorithms":[162],"for":[163,179,212],"it":[164],"arbitrary":[166],"networks.":[168],"Results:":[169],"In":[170],"this":[171],"work,":[172],"we":[173],"present":[174],"computer":[177],"program":[178,183,208],"CCP.":[181],"developed":[185],"basis":[188],"linear-time":[191],"transformation":[192],"small":[195],"version":[196],"SAT":[202],"problem.":[203],"Availability":[204],"implementation:":[206],"package":[209],"available":[211],"download":[213],"http://www.math.nus.edu.sg/\u223cmatzlx/ccp.":[215]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
