{"id":"https://openalex.org/W1986968252","doi":"https://doi.org/10.1186/s13015-014-0031-3","title":"EUCALYPT: efficient tree reconciliation enumerator","display_name":"EUCALYPT: efficient tree reconciliation enumerator","publication_year":2015,"publication_date":"2015-01-23","ids":{"openalex":"https://openalex.org/W1986968252","doi":"https://doi.org/10.1186/s13015-014-0031-3","mag":"1986968252","pmid":"https://pubmed.ncbi.nlm.nih.gov/25648467"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-014-0031-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-014-0031-3","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0031-3","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0031-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090539933","display_name":"Beatrice Donati","orcid":"https://orcid.org/0000-0002-4707-8476"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR","IT"],"is_corresponding":false,"raw_author_name":"Beatrice Donati","raw_affiliation_strings":["Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","Universit\u00e0 di Firenze, Dipartimento di Ingegneria dell'Informazione; Via Santa Marta, 3, Firenze, 50139 Italy","Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","Inria Grenoble - Rh\u00f4ne-Alpes","Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","institution_ids":["https://openalex.org/I4210101348"]},{"raw_affiliation_string":"Universit\u00e0 di Firenze, Dipartimento di Ingegneria dell'Informazione; Via Santa Marta, 3, Firenze, 50139 Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I4210101348","https://openalex.org/I899635006"]},{"raw_affiliation_string":"Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047766466","display_name":"Christian Baudet","orcid":"https://orcid.org/0000-0002-9187-6512"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christian Baudet","raw_affiliation_strings":["Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334, France","Inria Grenoble - Rh\u00f4ne-Alpes"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","institution_ids":["https://openalex.org/I4210101348"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334, France","institution_ids":[]},{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I4210101348","https://openalex.org/I899635006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027309652","display_name":"Blerina Sinaimeri","orcid":"https://orcid.org/0000-0002-9797-7592"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Blerina Sinaimeri","raw_affiliation_strings":["Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334, France","Inria Grenoble - Rh\u00f4ne-Alpes"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","institution_ids":["https://openalex.org/I4210101348"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334, France","institution_ids":[]},{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes","institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I4210101348","https://openalex.org/I899635006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012362492","display_name":"Pierluigi Crescenzi","orcid":"https://orcid.org/0000-0001-8789-3195"},"institutions":[{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pierluigi Crescenzi","raw_affiliation_strings":["Universit\u00e0 di Firenze, Dipartimento di Ingegneria dell'Informazione; Via Santa Marta, 3, Firenze, 50139 Italy","Via Santa Marta, 3, Firenze, 50139, Italy","Universit\u00e0 di Firenze, Dipartimento di Ingegneria dell'Informazione"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e0 di Firenze, Dipartimento di Ingegneria dell'Informazione; Via Santa Marta, 3, Firenze, 50139 Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Via Santa Marta, 3, Firenze, 50139, Italy","institution_ids":[]},{"raw_affiliation_string":"Universit\u00e0 di Firenze, Dipartimento di Ingegneria dell'Informazione","institution_ids":["https://openalex.org/I45084792"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110531794","display_name":"Marie-France Sagot","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marie-France Sagot","raw_affiliation_strings":["Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","CNRS, UMR5558","Universit\u00e9 Lyon 1","Universit\u00e9 de Lyon, F-69000, Lyon","43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria Grenoble - Rh\u00f4ne-Alpes; Inovall\u00e9e 655, avenue de l'Europe, Montbonnot, Saint Ismier cedex, 38334 France","institution_ids":["https://openalex.org/I4210101348"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558; 43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622 France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"CNRS, UMR5558","institution_ids":[]},{"raw_affiliation_string":"Universit\u00e9 Lyon 1","institution_ids":["https://openalex.org/I100532134"]},{"raw_affiliation_string":"Universit\u00e9 de Lyon, F-69000, Lyon","institution_ids":["https://openalex.org/I100532134"]},{"raw_affiliation_string":"43 Boulevard du 11 Novembre 1918, Villeurbanne cedex, 69622, France","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":1.958,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.86001715,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7307999730110168,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7307999730110168,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.14429999887943268,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.013799999840557575,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.678191065788269},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.668083667755127},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6195470094680786},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6190359592437744},{"id":"https://openalex.org/keywords/enumeration","display_name":"Enumeration","score":0.5991095304489136},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.561895489692688},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.5567589998245239},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.45073169469833374},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.44445669651031494},{"id":"https://openalex.org/keywords/coevolution","display_name":"Coevolution","score":0.4220002293586731},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3365626931190491},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3301827907562256},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.27134525775909424},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2538696825504303},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10834705829620361},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.09501498937606812}],"concepts":[{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.678191065788269},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.668083667755127},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6195470094680786},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6190359592437744},{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.5991095304489136},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.561895489692688},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.5567589998245239},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.45073169469833374},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.44445669651031494},{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.4220002293586731},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3365626931190491},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3301827907562256},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.27134525775909424},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2538696825504303},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10834705829620361},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.09501498937606812},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1186/s13015-014-0031-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-014-0031-3","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0031-3","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:25648467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25648467","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.683.3125","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.683.3125","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://almob.org/content/download/supplementary/s13015-014-0031-3-s1.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:hal-01092977v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-01092977","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, 2015, 10 (1), pp.11. &#x27E8;10.1186/s13015-014-0031-3&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:3282523","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4310143","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:flore.unifi.it:2158/1041113","is_oa":true,"landing_page_url":"http://hdl.handle.net/2158/1041113","pdf_url":null,"source":{"id":"https://openalex.org/S4306402033","display_name":"Florence Research (University of Florence)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45084792","host_organization_name":"University of Florence","host_organization_lineage":["https://openalex.org/I45084792"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.luiss.it:11385/202497","is_oa":true,"landing_page_url":"http://hdl.handle.net/11385/202497","pdf_url":null,"source":{"id":"https://openalex.org/S4377196446","display_name":"IRIS - Institutional Research Information System (Libera Universit\u00e0 Internazionale degli Studi Sociali Guido Carli)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56441308","host_organization_name":"Libera Universit\u00e0 Internazionale degli Studi Sociali Guido Carli","host_organization_lineage":["https://openalex.org/I56441308"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s13015-014-0031-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-014-0031-3","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0031-3","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3953001729","display_name":null,"funder_award_id":"2007-2013","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320330080","display_name":"Laboratoire d'Excellence Ecofect","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1986968252.pdf","grobid_xml":"https://content.openalex.org/works/W1986968252.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W16471194","https://openalex.org/W60927400","https://openalex.org/W92516518","https://openalex.org/W1570143449","https://openalex.org/W1594683133","https://openalex.org/W1970909551","https://openalex.org/W1992274351","https://openalex.org/W1992584622","https://openalex.org/W1996156981","https://openalex.org/W2008252897","https://openalex.org/W2032186263","https://openalex.org/W2034492097","https://openalex.org/W2038968181","https://openalex.org/W2046039468","https://openalex.org/W2067516627","https://openalex.org/W2076385002","https://openalex.org/W2091707359","https://openalex.org/W2094002760","https://openalex.org/W2097059816","https://openalex.org/W2110014387","https://openalex.org/W2112755610","https://openalex.org/W2116433762","https://openalex.org/W2119670789","https://openalex.org/W2128520958","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2144345157","https://openalex.org/W2144454528","https://openalex.org/W2144619586","https://openalex.org/W2144898181","https://openalex.org/W2145608399","https://openalex.org/W2148231054","https://openalex.org/W2166106146","https://openalex.org/W2169802620","https://openalex.org/W2962870524"],"related_works":["https://openalex.org/W108845024","https://openalex.org/W4300125793","https://openalex.org/W2578985712","https://openalex.org/W2406961474","https://openalex.org/W2143566611","https://openalex.org/W2013740965","https://openalex.org/W588267724","https://openalex.org/W4297743441","https://openalex.org/W124046120","https://openalex.org/W3173815060"],"abstract_inverted_index":{"BACKGROUND:":[0],"Phylogenetic":[1],"tree":[2,30,34],"reconciliation":[3],"is":[4,109,113,121,179,329,344],"the":[5,11,28,32,44,65,95,119,125,175,220,233,244,288,297,304,320,323],"approach":[6],"of":[7,13,15,56,106,127,137,166,177,199,202,209,212,222,249,252,299],"choice":[8],"for":[9,43,145,163,232,338],"investigating":[10],"coevolution":[12],"sets":[14],"organisms":[16],"such":[17,82],"as":[18,308,310],"hosts":[19],"and":[20,31,118,251,266],"parasites.":[21],"It":[22],"consists":[23],"in":[24,84,94,135,153,197,230,322],"a":[25,40,72,142,268,316,335],"mapping":[26],"between":[27,279],"parasite":[29],"host":[33,272,289],"using":[35],"event-based":[36],"maximum":[37],"parsimony.":[38],"Given":[39],"cost":[41,99,238,245,317],"model":[42],"events,":[45],"many":[46,155,201],"optimal":[47,70,148,306,321,341],"reconciliations":[48,342],"are":[49,91,101,186,194,274,282],"however":[50],"possible.":[51],"Any":[52],"further":[53,259],"biological":[54],"interpretation":[55],"them":[57],"must":[58],"therefore":[59],"take":[60],"this":[61,107,116,262],"into":[62],"account,":[63],"making":[64],"capacity":[66],"to":[67,114,122,276,295,311,319],"enumerate":[68],"all":[69,88,98,147,340],"solutions":[71,90,128,156,178,193,213,250,301,314],"crucial":[73],"point.":[74],"Only":[75],"two":[76,164],"algorithms":[77],"currently":[78,102],"exist":[79],"that":[80,152,281],"attempt":[81],"enumeration;":[83],"one":[85],"case":[86],"not":[87,97],"possible":[89],"produced":[92],"while":[93,302],"other":[96],"vectors":[100],"handled.":[103],"The":[104,111,207],"objective":[105],"paper":[108],"two-fold.":[110],"first":[112],"fill":[115],"gap,":[117],"second":[120],"test":[123],"whether":[124],"number":[126,176,208,221,298],"generally":[129],"observed":[130],"can":[131],"be":[132,216],"an":[133,160],"issue":[134],"terms":[136,198],"interpretation.":[138],"RESULTS:":[139],"We":[140,150,158,332],"present":[141,333],"polynomial-delay":[143,336],"algorithm":[144,337],"enumerating":[146,339],"reconciliations.":[149],"show":[151],"general":[154],"exist.":[157],"give":[159],"example":[161],"where,":[162],"pairs":[165],"host-parasite":[167],"trees":[168],"having":[169],"each":[170,203],"less":[171],"than":[172,219],"41":[173],"leaves,":[174],"5120,":[180],"even":[181],"when":[182],"only":[183,278],"time-feasible":[184,300,313,327],"ones":[185],"kept.":[187],"To":[188,258],"facilitate":[189],"their":[190],"interpretation,":[191],"those":[192],"also":[195],"classified":[196],"how":[200],"event":[204],"they":[205,225],"contain.":[206],"different":[210],"classes":[211,253],"may":[214,226,255],"thus":[215],"notably":[217],"smaller":[218],"solutions,":[223],"yet":[224],"remain":[227],"high":[228],"enough,":[229],"particular":[231],"cases":[234,324],"where":[235,271,325],"losses":[236],"have":[237],"0.":[239],"In":[240],"fact,":[241],"depending":[242],"on":[243],"vector,":[246],"both":[247],"numbers":[248],"thereof":[254],"increase":[256],"considerably.":[257],"deal":[260],"with":[261,315],"problem,":[263],"we":[264],"introduce":[265],"analyse":[267],"restricted":[269],"version":[270],"switches":[273],"allowed":[275],"happen":[277],"species":[280],"within":[283],"some":[284],"fixed":[285],"distance":[286],"along":[287],"tree.":[290],"This":[291],"restriction":[292],"allows":[293],"us":[294],"reduce":[296],"preserving":[303],"same":[305],"cost,":[307],"well":[309],"find":[312],"close":[318],"no":[326],"solution":[328],"found.":[330],"CONCLUSIONS:":[331],"Eucalypt,":[334],"which":[343],"freely":[345],"available":[346],"at":[347],"http://eucalypt.gforge.inria.fr/.":[348]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
