{"id":"https://openalex.org/W2105669285","doi":"https://doi.org/10.1186/1748-7188-8-12","title":"Reconciliation and local gene tree rearrangement can be of mutual profit","display_name":"Reconciliation and local gene tree rearrangement can be of mutual profit","publication_year":2013,"publication_date":"2013-04-08","ids":{"openalex":"https://openalex.org/W2105669285","doi":"https://doi.org/10.1186/1748-7188-8-12","mag":"2105669285","pmid":"https://pubmed.ncbi.nlm.nih.gov/23566548"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-8-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-12","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-12","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/10.1186/1748-7188-8-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111382126","display_name":"Thi Hau Nguyen","orcid":null},"institutions":[{"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Thi Hau Nguyen","raw_affiliation_strings":["LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier C\u00e9dex 5, France. vberry@lirmm.fr","LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier C\u00e9dex 5, France. vberry@lirmm.fr","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]},{"raw_affiliation_string":"LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025043496","display_name":"Vincent Ranwez","orcid":"https://orcid.org/0000-0002-9308-7541"},"institutions":[{"id":"https://openalex.org/I24906876","display_name":"Institut Agro Montpellier","ror":"https://ror.org/03rnk6m14","country_code":"FR","type":"education","lineage":["https://openalex.org/I24906876","https://openalex.org/I4210117091","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210120904","display_name":"Am\u00e9lioration G\u00e9n\u00e9tique et Adaptation des Plantes m\u00e9diterran\u00e9ennes et tropicales","ror":"https://ror.org/02w4exq36","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210120904","https://openalex.org/I4399657933"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Ranwez","raw_affiliation_strings":["Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","Montpellier SupAgro (UMR AGAP), Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","institution_ids":[]},{"raw_affiliation_string":"Montpellier SupAgro (UMR AGAP), Montpellier, France","institution_ids":["https://openalex.org/I4210120904","https://openalex.org/I24906876"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031382311","display_name":"St\u00e9phanie Pointet","orcid":null},"institutions":[{"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9phanie Pointet","raw_affiliation_strings":["Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","institution_ids":[]},{"raw_affiliation_string":"LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113183324","display_name":"Anne-Muriel Arigon Chifolleau","orcid":null},"institutions":[{"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne-Muriel Arigon Chifolleau","raw_affiliation_strings":["Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","institution_ids":[]},{"raw_affiliation_string":"LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044582405","display_name":"Jean\u2010Philippe Doyon","orcid":null},"institutions":[{"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean-Philippe Doyon","raw_affiliation_strings":["Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","institution_ids":[]},{"raw_affiliation_string":"LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058327913","display_name":"Vincent Berry","orcid":"https://orcid.org/0000-0001-7271-4027"},"institutions":[{"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/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Berry","raw_affiliation_strings":["Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Biologie Computationnelle, 95 rue de la Gal\u00e9ra, 34095, Montpellier c\u00e9dex, France","institution_ids":[]},{"raw_affiliation_string":"LIRMM, UMR 5506 CNRS - Universit\u00e9 Montpellier 2, Montpellier, C\u00e9dex 5, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5111382126"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":3.6667,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.93179149,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.6980999708175659,"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":0.6980999708175659,"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":0.26179999113082886,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.01889999955892563,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7006612420082092},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6255131363868713},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5989203453063965},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.46344733238220215},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.461018443107605},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4587554931640625},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.42398083209991455},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3827768564224243},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38105693459510803},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37984466552734375},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2681275010108948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2645171880722046},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21521106362342834},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1953323781490326},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13512271642684937}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7006612420082092},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6255131363868713},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5989203453063965},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.46344733238220215},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.461018443107605},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4587554931640625},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.42398083209991455},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3827768564224243},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38105693459510803},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37984466552734375},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2681275010108948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2645171880722046},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21521106362342834},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1953323781490326},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13512271642684937},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1748-7188-8-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-12","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-12","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:23566548","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23566548","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:HAL:lirmm-00812726v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-00812726","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":"http://www.biomedcentral.com/","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:2856686","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3871789","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3871789","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3871789","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-8-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-12","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-12","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/G4455444033","display_name":null,"funder_award_id":"ANR-10-BINF-01-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2105669285.pdf","grobid_xml":"https://content.openalex.org/works/W2105669285.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W157609093","https://openalex.org/W1493206838","https://openalex.org/W1523611852","https://openalex.org/W1524445315","https://openalex.org/W1774207464","https://openalex.org/W1931647778","https://openalex.org/W1970909551","https://openalex.org/W1979257831","https://openalex.org/W1988471037","https://openalex.org/W1990812345","https://openalex.org/W2004575303","https://openalex.org/W2005059149","https://openalex.org/W2007802079","https://openalex.org/W2007850812","https://openalex.org/W2013067928","https://openalex.org/W2029133099","https://openalex.org/W2032299129","https://openalex.org/W2060425093","https://openalex.org/W2062354928","https://openalex.org/W2065375138","https://openalex.org/W2086585172","https://openalex.org/W2091918228","https://openalex.org/W2093999627","https://openalex.org/W2112755610","https://openalex.org/W2117000771","https://openalex.org/W2125359798","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2134824589","https://openalex.org/W2135281627","https://openalex.org/W2137604740","https://openalex.org/W2138113680","https://openalex.org/W2144345157","https://openalex.org/W2144454528","https://openalex.org/W2148231054","https://openalex.org/W2159368494","https://openalex.org/W2160690190","https://openalex.org/W2166106146","https://openalex.org/W2168696662","https://openalex.org/W2182410060","https://openalex.org/W2752061190","https://openalex.org/W2752853835","https://openalex.org/W4231886136","https://openalex.org/W4233815609","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4312203868","https://openalex.org/W2069013776","https://openalex.org/W2038264393","https://openalex.org/W2059637021","https://openalex.org/W2378282666","https://openalex.org/W2362218761","https://openalex.org/W2113708670","https://openalex.org/W2062354928","https://openalex.org/W2088120817","https://openalex.org/W2158340599"],"abstract_inverted_index":{"BACKGROUND:":[0],"Reconciliation":[1],"methods":[2,61,70,100],"compare":[3],"gene":[4,30,96,122,132,146,211,263,297,314],"trees":[5,8,31,147,212,224,298],"and":[6,17,22,83,112,135,164,225,250,318],"species":[7,305],"to":[9,41,62,74,119,183,188,220,227,243,278,286,326],"recover":[10],"evolutionary":[11,67],"events":[12],"such":[13,51,215,333],"as":[14,45,47,52],"duplications,":[15,133],"transfers":[16],"losses":[18,134],"explaining":[19],"the":[20,64,80,86,94,143,170,178,190,221,239,247,251,310,313,344],"history":[21],"composition":[23],"of":[24,66,106,253,260,271,312],"genomes.":[25],"It":[26],"is":[27,346],"well-known":[28],"that":[29,138,210,238,279],"inferred":[32,254],"from":[33],"molecular":[34],"sequences":[35],"can":[36,115,299],"be":[37,117,301],"partly":[38],"erroneous":[39],"due":[40],"incorrect":[42],"sequence":[43],"alignments":[44],"well":[46],"phylogenetic":[48],"reconstruction":[49],"artifacts":[50],"long":[53],"branch":[54],"attraction.":[55],"In":[56],"practice,":[57],"this":[58,76,265],"leads":[59,242],"reconciliation":[60,128,171,248,266],"overestimate":[63],"number":[65,252],"events.":[68,255],"Several":[69],"have":[71,101],"been":[72,102],"proposed":[73,240,280],"circumvent":[75],"problem,":[77],"by":[78,91,148,198,214,274,281],"collapsing":[79],"unsupported":[81],"edges":[82,158],"then":[84],"resolving":[85],"obtained":[87,323],"multifurcating":[88],"nodes,":[89],"or":[90],"directly":[92],"rearranging":[93,149],"binary":[95],"trees.":[97],"Yet":[98],"these":[99],"defined":[103],"for":[104,110,131,309,332],"models":[105],"evolution":[107],"accounting":[108,130,308,331],"only":[109],"duplications":[111],"losses,":[113],"i.e.":[114],"not":[116,330],"applied":[118],"handle":[120],"prokaryotic":[121,272],"families.":[123],"RESULTS:":[124],"We":[125,173],"propose":[126],"a":[127,160,244,258,269,282],"method":[129,241,267,345],"horizontal":[136],"transfers,":[137],"specifically":[139],"takes":[140],"into":[141],"account":[142],"uncertainties":[144,334],"in":[145,246],"their":[150,304],"weakly":[151],"supported":[152],"edges.":[153],"Rearrangements":[154],"are":[155,165,196,218,322],"performed":[156],"on":[157,177,206,231,234,257],"having":[159],"low":[161],"confidence":[162],"value,":[163],"accepted":[166],"whenever":[167],"they":[168],"improve":[169],"cost.":[172],"prove":[174],"useful":[175],"properties":[176],"dynamic":[179],"programming":[180],"matrix":[181],"used":[182],"compute":[184],"reconciliations,":[185],"which":[186],"allows":[187],"speed-up":[189],"tree":[191],"space":[192],"exploration":[193],"when":[194],"rearrangements":[195,217],"generated":[197],"Nearest":[199],"Neighbor":[200],"Interchanges":[201],"(NNI)":[202],"edit":[203],"operations.":[204],"Experiments":[205,233],"synthetic":[207],"data":[208,236],"show":[209],"modified":[213],"NNI":[216],"closer":[219],"correct":[222],"simulated":[223],"lead":[226],"better":[228],"event":[229],"predictions":[230],"average.":[232],"real":[235],"demonstrate":[237],"decrease":[245],"cost":[249],"Finally":[256],"dataset":[259],"30":[261],"k":[262],"families,":[264],"shows":[268],"ranking":[270],"phyla":[273],"transfer":[275,287],"rates":[276],"identical":[277],"different":[283],"approach":[284],"dedicated":[285],"detection":[288],"[BMCBIOINF":[289],"11:324,":[290],"2010,":[291,337],"PNAS":[292],"109(13):4962-4967,":[293],"2012].":[294],"CONCLUSIONS:":[295],"Prokaryotic":[296],"now":[300],"reconciled":[302],"with":[303,324],"phylogeny":[306],"while":[307],"uncertainty":[311],"tree.":[315],"More":[316],"accurate":[317],"more":[319],"precise":[320],"reconciliations":[321],"respect":[325],"previous":[327],"parsimony":[328],"algorithms":[329],"[LNCS":[335],"6398:93-108,":[336],"BIOINF":[338],"28(12):":[339],"i283-i291,":[340],"2012].A":[341],"software":[342],"implementing":[343],"freely":[347],"available":[348],"at":[349],"http://www.atgc-montpellier.fr/Mowgli/.":[350]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
