{"id":"https://openalex.org/W3017197234","doi":"https://doi.org/10.1186/s13015-020-00165-2","title":"From pairs of most similar sequences to phylogenetic best matches","display_name":"From pairs of most similar sequences to phylogenetic best matches","publication_year":2020,"publication_date":"2020-04-09","ids":{"openalex":"https://openalex.org/W3017197234","doi":"https://doi.org/10.1186/s13015-020-00165-2","mag":"3017197234"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-020-00165-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00165-2","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-020-00165-2","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-020-00165-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"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/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]},{"id":"https://openalex.org/I2801030728","display_name":"German Centre for Integrative Biodiversity Research","ror":"https://ror.org/01jty7g66","country_code":"DE","type":"facility","lineage":["https://openalex.org/I2801030728"]},{"id":"https://openalex.org/I36243813","display_name":"Universidad Nacional de Colombia","ror":"https://ror.org/059yx9a68","country_code":"CO","type":"education","lineage":["https://openalex.org/I36243813"]},{"id":"https://openalex.org/I4210091327","display_name":"Max Planck Institute for Mathematics in the Sciences","ror":"https://ror.org/00ez2he07","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210091327"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["AT","CO","DE","US"],"is_corresponding":true,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, 04107, Leipzig, Germany","Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Augustusplatz 12, 04107, Leipzig, Germany","Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria","Facultad de Ciencias, Universidad National de Colombia, Sede Bogot\u00e1, Ciudad Universitaria, 111321, Bogot\u00e1, D.C., Colombia","Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 04103, Leipzig, Germany","Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA"],"raw_orcid":"https://orcid.org/0000-0002-5016-5191","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Augustusplatz 12, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I2801030728","https://openalex.org/I926574661"]},{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Facultad de Ciencias, Universidad National de Colombia, Sede Bogot\u00e1, Ciudad Universitaria, 111321, Bogot\u00e1, D.C., Colombia","institution_ids":["https://openalex.org/I36243813"]},{"raw_affiliation_string":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I4210091327"]},{"raw_affiliation_string":"Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA","institution_ids":["https://openalex.org/I1308548392"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066710728","display_name":"Manuela Gei\u00df","orcid":"https://orcid.org/0000-0002-4134-6820"},"institutions":[{"id":"https://openalex.org/I4210126338","display_name":"Software Competence Center Hagenberg (Austria)","ror":"https://ror.org/02ks3nr96","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210126338"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["AT","DE"],"is_corresponding":false,"raw_author_name":"Manuela Gei\u00df","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, 04107, Leipzig, Germany","Software Competence Center Hagenberg GmbH, Softwarepark 21, 4232, Hagenberg, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Software Competence Center Hagenberg GmbH, Softwarepark 21, 4232, Hagenberg, Austria","institution_ids":["https://openalex.org/I4210126338"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088739752","display_name":"David Schaller","orcid":"https://orcid.org/0000-0002-0025-3097"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"David Schaller","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, 04107, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054436008","display_name":"Alitzel L\u00f3pez S\u00e1nchez","orcid":"https://orcid.org/0000-0002-3545-039X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alitzel L\u00f3pez S\u00e1nchez","raw_affiliation_strings":["CONACYT-Instituto de Matem\u00e1ticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Quer\u00e9taro, QRO, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CONACYT-Instituto de Matem\u00e1ticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Quer\u00e9taro, QRO, M\u00e9xico","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067560070","display_name":"Marcos Gonz\u00e1lez Laffitte","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marcos Gonz\u00e1lez Laffitte","raw_affiliation_strings":["CONACYT-Instituto de Matem\u00e1ticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Quer\u00e9taro, QRO, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CONACYT-Instituto de Matem\u00e1ticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Quer\u00e9taro, QRO, M\u00e9xico","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081293756","display_name":"Dulce I. Valdivia","orcid":"https://orcid.org/0000-0002-7702-652X"},"institutions":[{"id":"https://openalex.org/I68368234","display_name":"Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional","ror":"https://ror.org/009eqmr18","country_code":"MX","type":"facility","lineage":["https://openalex.org/I59361560","https://openalex.org/I68368234"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Dulce I. Valdivia","raw_affiliation_strings":["Departamento de Ingenier\u00eda Gen\u00e9tica, Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN (CINVESTAV), Km. 9.6 Libramiento Norte Carretera Irapuato-Le\u00f3n, 36821, Irapuato, GTO, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Ingenier\u00eda Gen\u00e9tica, Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN (CINVESTAV), Km. 9.6 Libramiento Norte Carretera Irapuato-Le\u00f3n, 36821, Irapuato, GTO, M\u00e9xico","institution_ids":["https://openalex.org/I68368234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019719296","display_name":"Marc Hellmuth","orcid":"https://orcid.org/0000-0002-1620-5508"},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marc Hellmuth","raw_affiliation_strings":["School of Computing, University of Leeds, E C Stoner Building, Leeds, LS2 9JT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, University of Leeds, E C Stoner Building, Leeds, LS2 9JT, UK","institution_ids":["https://openalex.org/I130828816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037904080","display_name":"Maribel Hern\u00e1ndez-Rosales","orcid":"https://orcid.org/0000-0003-1878-1223"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maribel Hern\u00e1ndez Rosales","raw_affiliation_strings":["CONACYT-Instituto de Matem\u00e1ticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Quer\u00e9taro, QRO, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CONACYT-Instituto de Matem\u00e1ticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Quer\u00e9taro, QRO, M\u00e9xico","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5016104736"],"corresponding_institution_ids":["https://openalex.org/I129774422","https://openalex.org/I1308548392","https://openalex.org/I2801030728","https://openalex.org/I36243813","https://openalex.org/I4210091327","https://openalex.org/I926574661"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1494,"currency":"EUR","value_usd":1611},"fwci":0.917,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.72772558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"15","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9969000220298767,"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"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9922999739646912,"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/outgroup","display_name":"Outgroup","score":0.6442283391952515},{"id":"https://openalex.org/keywords/reciprocal","display_name":"Reciprocal","score":0.6435454487800598},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6261205673217773},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6064813733100891},{"id":"https://openalex.org/keywords/ultrametric-space","display_name":"Ultrametric space","score":0.6021993160247803},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5586597323417664},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5382117629051208},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4980456829071045},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4809636175632477},{"id":"https://openalex.org/keywords/a-priori-and-a-posteriori","display_name":"A priori and a posteriori","score":0.4714922606945038},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4673514664173126},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4567407965660095},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.4406796395778656},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4045003354549408},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37059324979782104},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3477620482444763},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3248688876628876},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23430979251861572},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22029706835746765},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21299564838409424},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.17668211460113525},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.12161386013031006}],"concepts":[{"id":"https://openalex.org/C51271553","wikidata":"https://www.wikidata.org/wiki/Q842917","display_name":"Outgroup","level":2,"score":0.6442283391952515},{"id":"https://openalex.org/C2777742833","wikidata":"https://www.wikidata.org/wiki/Q1964083","display_name":"Reciprocal","level":2,"score":0.6435454487800598},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6261205673217773},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6064813733100891},{"id":"https://openalex.org/C61067352","wikidata":"https://www.wikidata.org/wiki/Q1897429","display_name":"Ultrametric space","level":3,"score":0.6021993160247803},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5586597323417664},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5382117629051208},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4980456829071045},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4809636175632477},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.4714922606945038},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4673514664173126},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4567407965660095},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.4406796395778656},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4045003354549408},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37059324979782104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3477620482444763},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3248688876628876},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23430979251861572},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22029706835746765},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21299564838409424},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.17668211460113525},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.12161386013031006},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C198043062","wikidata":"https://www.wikidata.org/wiki/Q180953","display_name":"Metric space","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-020-00165-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00165-2","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-020-00165-2","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":"pmh:oai:eprints.whiterose.ac.uk:160255","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:b2d7a667623a4363a60d45f12cc82c93","is_oa":true,"landing_page_url":"https://doaj.org/article/b2d7a667623a4363a60d45f12cc82c93","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-20 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7147060","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7147060","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/s13015-020-00165-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00165-2","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-020-00165-2","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G1254183670","display_name":null,"funder_award_id":"031A538A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G5414197814","display_name":null,"funder_award_id":"278966 FONCICYT 2","funder_id":"https://openalex.org/F4320321739","funder_display_name":"Consejo Nacional de Ciencia y Tecnolog\u00eda"},{"id":"https://openalex.org/G5828315659","display_name":null,"funder_award_id":"031A538A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6051632014","display_name":null,"funder_award_id":"de.NBI/RB 031A538A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321739","display_name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","ror":"https://ror.org/059ex5q34"},{"id":"https://openalex.org/F4320324635","display_name":"Fondo de Cooperaci\u00f3n Internacional en Ciencia y Tecnolog\u00eda","ror":"https://ror.org/059ex5q34"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3017197234.pdf","grobid_xml":"https://content.openalex.org/works/W3017197234.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W319819633","https://openalex.org/W1525734744","https://openalex.org/W1575387405","https://openalex.org/W1771294277","https://openalex.org/W1928030931","https://openalex.org/W1967621400","https://openalex.org/W1974906551","https://openalex.org/W1979835060","https://openalex.org/W1990453950","https://openalex.org/W1995117714","https://openalex.org/W1996490834","https://openalex.org/W2005471817","https://openalex.org/W2009234149","https://openalex.org/W2009596137","https://openalex.org/W2020184108","https://openalex.org/W2022221380","https://openalex.org/W2038876634","https://openalex.org/W2040940215","https://openalex.org/W2041386815","https://openalex.org/W2041863586","https://openalex.org/W2049349724","https://openalex.org/W2062018285","https://openalex.org/W2065461553","https://openalex.org/W2067547496","https://openalex.org/W2075503802","https://openalex.org/W2076595168","https://openalex.org/W2078109763","https://openalex.org/W2078650268","https://openalex.org/W2082176153","https://openalex.org/W2082445660","https://openalex.org/W2085822559","https://openalex.org/W2094939159","https://openalex.org/W2097706568","https://openalex.org/W2099388422","https://openalex.org/W2101783948","https://openalex.org/W2104056950","https://openalex.org/W2104268875","https://openalex.org/W2104998102","https://openalex.org/W2114368970","https://openalex.org/W2114850508","https://openalex.org/W2117748102","https://openalex.org/W2126423997","https://openalex.org/W2132985118","https://openalex.org/W2136525653","https://openalex.org/W2137057090","https://openalex.org/W2138140955","https://openalex.org/W2143210482","https://openalex.org/W2145100181","https://openalex.org/W2152075687","https://openalex.org/W2152886327","https://openalex.org/W2154044807","https://openalex.org/W2155418451","https://openalex.org/W2155587511","https://openalex.org/W2159266221","https://openalex.org/W2166106146","https://openalex.org/W2167539386","https://openalex.org/W2316262244","https://openalex.org/W2415398545","https://openalex.org/W2734735318","https://openalex.org/W2734849906","https://openalex.org/W2743986353","https://openalex.org/W2765127695","https://openalex.org/W2794905278","https://openalex.org/W2809155103","https://openalex.org/W2951126701","https://openalex.org/W2963087067","https://openalex.org/W2963102422","https://openalex.org/W2987931166","https://openalex.org/W2998742065","https://openalex.org/W3004232123","https://openalex.org/W3098656959","https://openalex.org/W4206702770","https://openalex.org/W4388212639"],"related_works":["https://openalex.org/W4287598215","https://openalex.org/W3105794585","https://openalex.org/W4236333616","https://openalex.org/W2999666600","https://openalex.org/W2054856023","https://openalex.org/W4245978557","https://openalex.org/W4285726363","https://openalex.org/W1612061217","https://openalex.org/W2915589228","https://openalex.org/W4294578906"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Many":[2],"of":[3,17,31,38,76,108,128,136,200,205,216,220,232],"the":[4,51,79,115,119,134,137,141,147,217,230],"commonly":[5],"used":[6],"methods":[7,209],"for":[8,25,46,82],"orthology":[9,84,207,238],"detection":[10,85],"start":[11],"from":[12,184,213],"mutually":[13],"most":[14,27,97],"similar":[15],"pairs":[16,30,100],"genes":[18,32,92,109,122],"(reciprocal":[19,33],"best":[20,34,39,42,201,221,234],"hits)":[21],"as":[22],"an":[23],"approximation":[24,37],"evolutionary":[26,96],"closely":[28,98],"related":[29,99],"matches).":[35],"This":[36],"matches":[40,222],"by":[41,104],"hits":[43],"becomes":[44],"exact":[45],"ultrametric":[47],"dissimilarities,":[48],"i.e.,":[49],"under":[50],"Molecular":[52],"Clock":[53],"Hypothesis.":[54],"It":[55],"fails,":[56],"however,":[57],"whenever":[58],"there":[59],"are":[60,93,189],"large":[61],"lineage":[62,159],"specific":[63,160],"rate":[64,163],"variations":[65],"among":[66],"paralogous":[67],"genes.":[68],"In":[69,173],"practice,":[70],"this":[71],"introduces":[72],"a":[73,144,174,214],"high":[74],"level":[75],"noise":[77],"into":[78],"input":[80],"data":[81,179,186],"best-hit-based":[83],"methods.":[86],"Results":[87],"If":[88],"additive":[89],"distances":[90,178],"between":[91],"known,":[94],"then":[95],"can":[101,170,210],"be":[102,151,171,182,211],"identified":[103],"considering":[105],"certain":[106],"quartets":[107],"provided":[110],"that":[111,166],"in":[112,154,229],"each":[113],"quartet":[114],"outgroup":[116,149],"relative":[117],"to":[118,181,195],"remaining":[120],"three":[121],"is":[123,192,243],"known.":[124],"A":[125],"priori":[126],"knowledge":[127],"underlying":[129],"species":[130],"phylogeny":[131],"greatly":[132],"facilitates":[133],"identification":[135],"required":[138],"outgroup.":[139],"Although":[140],"workflow":[142],"remains":[143],"heuristic":[145],"since":[146],"correct":[148],"cannot":[150],"determined":[152],"reliably":[153],"all":[155],"cases,":[156],"simulations":[157],"with":[158],"biases":[161],"and":[162,187,225,237],"asymmetries":[164],"show":[165],"nearly":[167],"perfect":[168],"results":[169],"achieved.":[172],"realistic":[175],"setting,":[176],"where":[177],"have":[180],"estimated":[183],"sequence":[185],"hence":[188],"noisy,":[190],"it":[191],"still":[193],"possible":[194],"obtain":[196],"highly":[197],"accurate":[198,218],"sets":[199],"matches.":[202],"Conclusion":[203],"Improvements":[204],"tree-free":[206],"assessment":[208],"expected":[212],"combination":[215],"inference":[219],"reported":[223],"here":[224],"recent":[226],"mathematical":[227],"advances":[228],"understanding":[231],"(reciprocal)":[233],"match":[235],"graphs":[236],"relations.":[239],"Availability":[240],"Accompanying":[241],"software":[242],"available":[244],"at":[245],"https://github.com/david-schaller/AsymmeTree":[246],".":[247]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
