{"id":"https://openalex.org/W2211903126","doi":"https://doi.org/10.1017/s1471068415000265","title":"Optimizing phylogenetic supertrees using answer set programming","display_name":"Optimizing phylogenetic supertrees using answer set programming","publication_year":2015,"publication_date":"2015-07-01","ids":{"openalex":"https://openalex.org/W2211903126","doi":"https://doi.org/10.1017/s1471068415000265","mag":"2211903126"},"language":"en","primary_location":{"id":"doi:10.1017/s1471068415000265","is_oa":false,"landing_page_url":"https://doi.org/10.1017/s1471068415000265","pdf_url":null,"source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1507.05272","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"LAURA KOPONEN","orcid":null},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"LAURA KOPONEN","raw_affiliation_strings":["HIIT and Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 AALTO, Finland (e-mail:"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HIIT and Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 AALTO, Finland (e-mail:","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":null,"display_name":"EMILIA OIKARINEN","orcid":null},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"EMILIA OIKARINEN","raw_affiliation_strings":["HIIT and Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 AALTO, Finland (e-mail:"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HIIT and Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 AALTO, Finland (e-mail:","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":null,"display_name":"TOMI JANHUNEN","orcid":null},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"TOMI JANHUNEN","raw_affiliation_strings":["HIIT and Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 AALTO, Finland (e-mail:"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HIIT and Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 AALTO, Finland (e-mail:","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"last","author":{"id":null,"display_name":"LAURA S\u00c4IL\u00c4","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"LAURA S\u00c4IL\u00c4","raw_affiliation_strings":["Department of Geosciences and Geography, University of HelsinkiP.O. Box 64, FI-00014 University of Helsinki, Finland (e-mail:"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Geosciences and Geography, University of HelsinkiP.O. Box 64, FI-00014 University of Helsinki, Finland (e-mail:","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9647,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.75219278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"15","issue":"4-5","first_page":"604","last_page":"619"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6150000095367432,"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":0.6150000095367432,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.04830000177025795,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.04179999977350235,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/supertree","display_name":"Supertree","score":0.9969000220298767},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6419000029563904},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6265000104904175},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5799999833106995},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5547999739646912},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.46470001339912415},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.462799996137619},{"id":"https://openalex.org/keywords/supermatrix","display_name":"Supermatrix","score":0.4275999963283539},{"id":"https://openalex.org/keywords/divide-and-conquer-algorithms","display_name":"Divide and conquer algorithms","score":0.40400001406669617}],"concepts":[{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.9969000220298767},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6949999928474426},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6419000029563904},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6265000104904175},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5799999833106995},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5547999739646912},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48890000581741333},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.46470001339912415},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.462799996137619},{"id":"https://openalex.org/C123439655","wikidata":"https://www.wikidata.org/wiki/Q3977978","display_name":"Supermatrix","level":5,"score":0.4275999963283539},{"id":"https://openalex.org/C71559656","wikidata":"https://www.wikidata.org/wiki/Q671298","display_name":"Divide and conquer algorithms","level":2,"score":0.40400001406669617},{"id":"https://openalex.org/C103275481","wikidata":"https://www.wikidata.org/wiki/Q6787889","display_name":"Matrix representation","level":3,"score":0.3910999894142151},{"id":"https://openalex.org/C57900377","wikidata":"https://www.wikidata.org/wiki/Q7979855","display_name":"Weight-balanced tree","level":4,"score":0.3837999999523163},{"id":"https://openalex.org/C182620335","wikidata":"https://www.wikidata.org/wiki/Q2852531","display_name":"Answer set programming","level":3,"score":0.3785000145435333},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.3736000061035156},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36559998989105225},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.335999995470047},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.3125999867916107},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.30889999866485596},{"id":"https://openalex.org/C110332635","wikidata":"https://www.wikidata.org/wiki/Q629498","display_name":"Genetic programming","level":2,"score":0.30869999527931213},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.29750001430511475},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.2782999873161316},{"id":"https://openalex.org/C52692508","wikidata":"https://www.wikidata.org/wiki/Q1333872","display_name":"Combinatorial optimization","level":2,"score":0.27469998598098755},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.27219998836517334},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.25279998779296875},{"id":"https://openalex.org/C137836250","wikidata":"https://www.wikidata.org/wiki/Q984063","display_name":"Optimization problem","level":2,"score":0.25119999051094055},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.25049999356269836}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1017/s1471068415000265","is_oa":false,"landing_page_url":"https://doi.org/10.1017/s1471068415000265","pdf_url":null,"source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1507.05272","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1507.05272","pdf_url":"https://arxiv.org/pdf/1507.05272","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:aaltodoc.aalto.fi:123456789/35686","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/910c6e57-c7a6-4bcd-ac8d-f1d33cb3ef7b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401662","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1507.05272","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1507.05272","pdf_url":"https://arxiv.org/pdf/1507.05272","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W5815757","https://openalex.org/W160062981","https://openalex.org/W1482532598","https://openalex.org/W1555875095","https://openalex.org/W1566423428","https://openalex.org/W1606891084","https://openalex.org/W1991405010","https://openalex.org/W1997780525","https://openalex.org/W2010954390","https://openalex.org/W2014087252","https://openalex.org/W2033854905","https://openalex.org/W2036921810","https://openalex.org/W2078109763","https://openalex.org/W2083213362","https://openalex.org/W2084289491","https://openalex.org/W2084895856","https://openalex.org/W2094277888","https://openalex.org/W2117221169","https://openalex.org/W2118058771","https://openalex.org/W2126763909","https://openalex.org/W2130887463","https://openalex.org/W2134117083","https://openalex.org/W2143720447","https://openalex.org/W2161909415","https://openalex.org/W2170052973","https://openalex.org/W2185680923","https://openalex.org/W2315781448","https://openalex.org/W2579372702","https://openalex.org/W4205112646","https://openalex.org/W4211177236","https://openalex.org/W4250071703","https://openalex.org/W4250164480","https://openalex.org/W6681295570"],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"The":[1,92],"supertree":[2,83,129],"construction":[3,84],"problem":[4,51,85],"is":[5,53,94],"about":[6],"combining":[7],"several":[8],"phylogenetic":[9],"trees":[10,27,43,101,117],"with":[11,40,64],"possibly":[12],"conflicting":[13],"information":[14],"into":[15],"a":[16,127],"single":[17],"tree":[18],"that":[19,52],"has":[20],"all":[21],"the":[22,25,32,35,41,74,82,108,113,131,146],"leaves":[23,30,36],"of":[24,76,88,100,133],"source":[26,42],"as":[28,38,44,61,105],"its":[29],"and":[31,56],"relationships":[33,114],"between":[34],"are":[37,67],"consistent":[39],"possible.":[45],"This":[46],"leads":[47],"to":[48,80,125,141],"an":[49,97],"optimization":[50],"computationally":[54],"challenging":[55],"typically":[57],"heuristic":[58],"methods,":[59],"such":[60],"matrix":[62],"representation":[63],"parsimony":[65],"(MRP),":[66],"used.":[68],"In":[69],"this":[70],"paper":[71],"we":[72,137],"consider":[73],"use":[75,122],"answer":[77],"set":[78],"programming":[79],"solve":[81],"in":[86,116],"terms":[87],"two":[89],"alternative":[90],"encodings.":[91],"first":[93],"based":[95],"on":[96],"existing":[98],"encoding":[99,111],"using":[102],"substructures":[103],"known":[104],"quartets,":[106],"while":[107],"other":[109],"novel":[110],"captures":[112],"present":[115],"through":[118],"direct":[119],"projections.":[120],"We":[121],"these":[123],"encodings":[124],"compute":[126],"genus-level":[128],"for":[130],"family":[132],"cats":[134],"(Felidae).":[135],"Furthermore,":[136],"compare":[138],"our":[139],"results":[140],"recent":[142],"supertrees":[143],"obtained":[144],"by":[145],"MRP":[147],"method.":[148]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2016-06-24T00:00:00"}
