{"id":"https://openalex.org/W2103513093","doi":"https://doi.org/10.1093/bioinformatics/bti713","title":"Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood","display_name":"Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood","publication_year":2005,"publication_date":"2005-10-18","ids":{"openalex":"https://openalex.org/W2103513093","doi":"https://doi.org/10.1093/bioinformatics/bti713","mag":"2103513093","pmid":"https://pubmed.ncbi.nlm.nih.gov/16234323"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti713","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti713","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053511679","display_name":"Wim Hordijk","orcid":"https://orcid.org/0000-0002-0223-6194"},"institutions":[{"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/I4412460525"]},{"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/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Wim Hordijk","raw_affiliation_strings":["Projet M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM, UMR CNRS 5506, Universit\u00e9 Montpellier 2 \u00a0 161 rue Ada, 34392 Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Projet M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM, UMR CNRS 5506, Universit\u00e9 Montpellier 2 \u00a0 161 rue Ada, 34392 Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078068308","display_name":"Olivier Gascuel","orcid":"https://orcid.org/0000-0002-9412-9723"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"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/I4412460525"]},{"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Gascuel","raw_affiliation_strings":["Projet M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM, UMR CNRS 5506, Universit\u00e9 Montpellier 2 \u00a0 161 rue Ada, 34392 Montpellier, France"],"affiliations":[{"raw_affiliation_string":"Projet M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM, UMR CNRS 5506, Universit\u00e9 Montpellier 2 \u00a0 161 rue Ada, 34392 Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I1294671590","https://openalex.org/I4210101743"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053511679"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.1644,"has_fulltext":false,"cited_by_count":216,"citation_normalized_percentile":{"value":0.92057323,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"21","issue":"24","first_page":"4338","last_page":"4347"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9980000257492065,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.6961991786956787},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6741870641708374},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.58660888671875},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5841639041900635},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5431545972824097},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5288525819778442},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.4592646360397339},{"id":"https://openalex.org/keywords/likelihood-function","display_name":"Likelihood function","score":0.43500852584838867},{"id":"https://openalex.org/keywords/local-optimum","display_name":"Local optimum","score":0.4201608896255493},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.362761527299881},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.17543774843215942},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.12445232272148132},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.1202130913734436}],"concepts":[{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.6961991786956787},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6741870641708374},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.58660888671875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5841639041900635},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5431545972824097},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5288525819778442},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.4592646360397339},{"id":"https://openalex.org/C89106044","wikidata":"https://www.wikidata.org/wiki/Q45284","display_name":"Likelihood function","level":3,"score":0.43500852584838867},{"id":"https://openalex.org/C141934464","wikidata":"https://www.wikidata.org/wiki/Q3305386","display_name":"Local optimum","level":2,"score":0.4201608896255493},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.362761527299881},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.17543774843215942},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12445232272148132},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.1202130913734436},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","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":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bti713","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti713","pdf_url":null,"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:16234323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16234323","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:CiteSeerX.psu:10.1.1.60.6772","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.60.6772","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.lirmm.fr/mab/IMG/pdf/HordijkGascuel_BIOINF-2005.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:lirmm-00137439v1","is_oa":false,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-00137439","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2005, 21 (24), pp.4338-4347. ⟨10.1093/bioinformatics/bti713⟩","raw_type":"Journal articles"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W198692615","https://openalex.org/W240043582","https://openalex.org/W1498708571","https://openalex.org/W1538023365","https://openalex.org/W1546639740","https://openalex.org/W1561594449","https://openalex.org/W1867732144","https://openalex.org/W1990263013","https://openalex.org/W1993849326","https://openalex.org/W1999137142","https://openalex.org/W2010814032","https://openalex.org/W2016000389","https://openalex.org/W2037749900","https://openalex.org/W2038751597","https://openalex.org/W2048132103","https://openalex.org/W2062957956","https://openalex.org/W2070919193","https://openalex.org/W2074237174","https://openalex.org/W2078950386","https://openalex.org/W2097506564","https://openalex.org/W2099331099","https://openalex.org/W2101088466","https://openalex.org/W2102424972","https://openalex.org/W2103546861","https://openalex.org/W2103849916","https://openalex.org/W2105926960","https://openalex.org/W2117752525","https://openalex.org/W2120819924","https://openalex.org/W2122717632","https://openalex.org/W2124790653","https://openalex.org/W2128766881","https://openalex.org/W2131083844","https://openalex.org/W2150783480","https://openalex.org/W2157550858","https://openalex.org/W2161444534","https://openalex.org/W2164789250","https://openalex.org/W2246270786","https://openalex.org/W2408504390","https://openalex.org/W2994240441","https://openalex.org/W3032526099","https://openalex.org/W3199943451","https://openalex.org/W3217097258","https://openalex.org/W4247016878","https://openalex.org/W4254512069","https://openalex.org/W4388311318","https://openalex.org/W6629936565","https://openalex.org/W6639077426","https://openalex.org/W6675357019","https://openalex.org/W6691218616","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W2090308851","https://openalex.org/W2013921918","https://openalex.org/W2019724159","https://openalex.org/W4280508323","https://openalex.org/W2371672232","https://openalex.org/W3151346708","https://openalex.org/W2088686292","https://openalex.org/W2540019423","https://openalex.org/W2103185490","https://openalex.org/W2149766606"],"abstract_inverted_index":{"Experiments":[0],"with":[1,49],"real":[2],"datasets":[3],"comprising":[4],"35-250":[5],"taxa":[6],"show":[7],"that,":[8],"while":[9],"indeed":[10],"greatly":[11],"reducing":[12],"the":[13,29,58],"amount":[14],"of":[15,28],"computation,":[16],"our":[17,45],"approach":[18],"provides":[19],"likelihood":[20],"values":[21],"at":[22],"least":[23],"as":[24,26,53],"good":[25,63],"those":[27],"best-known":[30],"ML":[31],"methods":[32],"so":[33],"far":[34],"and":[35],"is":[36],"very":[37],"robust":[38],"to":[39,61],"poor":[40],"starting":[41],"trees.":[42],"Furthermore,":[43],"combining":[44],"new":[46],"SPR":[47],"algorithm":[48],"local":[50],"moves":[51],"such":[52],"PHYML's":[54],"nearest":[55],"neighbor":[56],"interchanges,":[57],"time":[59],"needed":[60],"find":[62],"solutions":[64],"can":[65],"sometimes":[66],"be":[67],"reduced":[68],"even":[69],"more.":[70]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":12}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}