{"id":"https://openalex.org/W2559493331","doi":"https://doi.org/10.1109/kse.2016.7758020","title":"A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation","display_name":"A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation","publication_year":2016,"publication_date":"2016-10-01","ids":{"openalex":"https://openalex.org/W2559493331","doi":"https://doi.org/10.1109/kse.2016.7758020","mag":"2559493331"},"language":"en","primary_location":{"id":"doi:10.1109/kse.2016.7758020","is_oa":false,"landing_page_url":"https://doi.org/10.1109/kse.2016.7758020","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 Eighth International Conference on Knowledge and Systems Engineering (KSE)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5025772345","display_name":"Diep Thi Hoang","orcid":"https://orcid.org/0000-0001-9200-2668"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Diep Thi Hoang","raw_affiliation_strings":["Faculty of Information Technology, University of Engineering and Technology, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, University of Engineering and Technology, Vietnam","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075478912","display_name":"L\u00ea S\u1ef9 Vinh","orcid":"https://orcid.org/0000-0002-9060-9199"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Le Sy Vinh","raw_affiliation_strings":["Faculty of Information Technology, University of Engineering and Technology, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, University of Engineering and Technology, Vietnam","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024578874","display_name":"Tom\u00e1\u0161 Flouri","orcid":"https://orcid.org/0000-0002-8474-9507"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]},{"id":"https://openalex.org/I71030271","display_name":"Heidelberg Institute for Theoretical Studies","ror":"https://ror.org/01f7bcy98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I71030271"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tomas Flouri","raw_affiliation_strings":["Heidelberg Institute for Theoretical Studies","Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Heidelberg Institute for Theoretical Studies","institution_ids":["https://openalex.org/I71030271"]},{"raw_affiliation_string":"Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025640090","display_name":"Alexandros Stamatakis","orcid":"https://orcid.org/0000-0003-0353-0691"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]},{"id":"https://openalex.org/I71030271","display_name":"Heidelberg Institute for Theoretical Studies","ror":"https://ror.org/01f7bcy98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I71030271"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexandros Stamatakis","raw_affiliation_strings":["Heidelberg Institute for Theoretical Studies","Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Heidelberg Institute for Theoretical Studies","institution_ids":["https://openalex.org/I71030271"]},{"raw_affiliation_string":"Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085983122","display_name":"Arndt von Haeseler","orcid":"https://orcid.org/0000-0002-3366-4458"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Arndt von Haeseler","raw_affiliation_strings":["Center for Integrative Bioinformatics Vienna, Medical University Vienna","Faculty of Computer Science, University of Vienna Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Medical University Vienna","institution_ids":["https://openalex.org/I76134821"]},{"raw_affiliation_string":"Faculty of Computer Science, University of Vienna Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019880902","display_name":"B\u00f9i Quang Minh","orcid":"https://orcid.org/0000-0002-5535-6560"},"institutions":[{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Bui Quang Minh","raw_affiliation_strings":["Center for Integrative Bioinformatics Vienna, Medical University Vienna"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Medical University Vienna","institution_ids":["https://openalex.org/I76134821"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.09566229,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9933000206947327,"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":0.9624000191688538,"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/bootstrapping","display_name":"Bootstrapping (finance)","score":0.8460764288902283},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"Maximum parsimony","score":0.6965424418449402},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.6295397281646729},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5239603519439697},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5173882246017456},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5156006217002869},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.510943591594696},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5086591839790344},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48179835081100464},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4621904790401459},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.43669992685317993},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.2953242063522339},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.19558194279670715},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11844819784164429},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.0908433198928833}],"concepts":[{"id":"https://openalex.org/C207609745","wikidata":"https://www.wikidata.org/wiki/Q4944086","display_name":"Bootstrapping (finance)","level":2,"score":0.8460764288902283},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.6965424418449402},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.6295397281646729},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5239603519439697},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5173882246017456},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5156006217002869},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.510943591594696},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5086591839790344},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48179835081100464},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4621904790401459},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.43669992685317993},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.2953242063522339},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.19558194279670715},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11844819784164429},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.0908433198928833},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/kse.2016.7758020","is_oa":false,"landing_page_url":"https://doi.org/10.1109/kse.2016.7758020","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 Eighth International Conference on Knowledge and Systems Engineering (KSE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W824229296","https://openalex.org/W1525734744","https://openalex.org/W1982447955","https://openalex.org/W1983102293","https://openalex.org/W2016000389","https://openalex.org/W2030517987","https://openalex.org/W2030966943","https://openalex.org/W2032476979","https://openalex.org/W2062018285","https://openalex.org/W2074237174","https://openalex.org/W2083213362","https://openalex.org/W2090493969","https://openalex.org/W2111211467","https://openalex.org/W2111647009","https://openalex.org/W2117897510","https://openalex.org/W2125359798","https://openalex.org/W2127836105","https://openalex.org/W2130727968","https://openalex.org/W2146058063","https://openalex.org/W2148294135","https://openalex.org/W2151692850","https://openalex.org/W2151949784","https://openalex.org/W2163892779","https://openalex.org/W2168696662","https://openalex.org/W3217097258","https://openalex.org/W4205208900","https://openalex.org/W4231648965","https://openalex.org/W4231784440","https://openalex.org/W4254275792","https://openalex.org/W6658468403","https://openalex.org/W6681941509"],"related_works":["https://openalex.org/W2963820820","https://openalex.org/W2520823390","https://openalex.org/W4300265711","https://openalex.org/W2963207658","https://openalex.org/W4401807688","https://openalex.org/W2090308851","https://openalex.org/W2362218761","https://openalex.org/W2375151634","https://openalex.org/W171301151","https://openalex.org/W2113708670"],"abstract_inverted_index":{"Reconstructing":[0],"maximum":[1,41],"parsimony":[2,60,82],"(MP)":[3],"trees":[4,51],"along":[5],"with":[6],"bootstrap":[7,30,64,87],"for":[8,27,40,62,101,110],"large":[9,111],"multiple":[10],"sequence":[11],"alignments":[12],"is":[13,74,123,135,142],"a":[14,24,36,85,121,137],"computationally":[15],"challenging":[16],"task.":[17],"In":[18],"this":[19],"paper,":[20],"we":[21],"present":[22],"MPBoot,":[23],"new":[25],"method":[26,39],"approximating":[28],"MP":[29],"based":[31],"on":[32,52,68],"the":[33,46,53,118,145,148],"idea":[34],"of":[35,113,147],"previously":[37],"introduced":[38],"likelihood":[42],"bootstrap.":[43],"MPBoot":[44,73,92,116,134],"economizes":[45],"computations":[47],"by":[48],"only":[49],"sampling":[50],"original":[54],"alignment":[55],"and":[56,79],"simultaneously":[57],"calculating":[58],"exact":[59],"scores":[61,83],"all":[63],"alignments.":[65],"Preliminary":[66],"experiments":[67],"simulated":[69,103],"data":[70,104],"showed":[71],"that":[72,120],"about":[75],"2-3.5":[76],"times":[77],"faster":[78],"yields":[80],"better":[81],"than":[84,99],"fast":[86],"procedure":[88],"implemented":[89],"in":[90,127],"TNT.":[91],"also":[93],"produced":[94],"less":[95],"biased":[96],"support":[97],"value":[98],"TNT":[100],"small":[102],"sets":[105],"(<;=":[106],"200":[107],"sequences).":[108],"However,":[109],"number":[112],"sequences":[114],"(>=500)":[115],"overestimates":[117],"probability":[119],"clade":[122],"true,":[124],"i.e.,":[125],"results":[126],"likely":[128],"high":[129],"false":[130],"positive":[131],"rates.":[132],"As":[133],"currently":[136],"proof-of-concept":[138],"implementation,":[139],"more":[140],"work":[141],"to":[143],"understand":[144],"limitations":[146],"method.":[149]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}