{"id":"https://openalex.org/W2101072339","doi":"https://doi.org/10.1093/bioinformatics/btt095","title":"Measuring guide-tree dependency of inferred gaps in progressive aligners","display_name":"Measuring guide-tree dependency of inferred gaps in progressive aligners","publication_year":2013,"publication_date":"2013-02-23","ids":{"openalex":"https://openalex.org/W2101072339","doi":"https://doi.org/10.1093/bioinformatics/btt095","mag":"2101072339","pmid":"https://pubmed.ncbi.nlm.nih.gov/23435067"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1011/48899209/bioinformatics_29_8_1011.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1011/48899209/bioinformatics_29_8_1011.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059757648","display_name":"Salvador Capella-Guti\u00e9rrez","orcid":"https://orcid.org/0000-0002-0309-604X"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Salvador Capella-Guti\u00e9rrez","raw_affiliation_strings":["1 Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88 and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88 and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I170486558","https://openalex.org/I4210137962"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003394700","display_name":"Toni Gabald\u00f3n","orcid":"https://orcid.org/0000-0003-0019-1735"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Toni Gabald\u00f3n","raw_affiliation_strings":["1 Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88 and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88 and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I170486558","https://openalex.org/I4210137962"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003394700"],"corresponding_institution_ids":["https://openalex.org/I170486558","https://openalex.org/I4210137962"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.9621,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.74796769,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"29","issue":"8","first_page":"1011","last_page":"1017"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8504999876022339,"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":0.8504999876022339,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.04320000112056732,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.006399999838322401,"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/tree","display_name":"Tree (set theory)","score":0.7555055618286133},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7339642643928528},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5866509675979614},{"id":"https://openalex.org/keywords/pairing","display_name":"Pairing","score":0.5354030132293701},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5327790975570679},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5242348313331604},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.482214093208313},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.43511587381362915},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4157133102416992},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37595346570014954},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32844066619873047},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31815797090530396},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16526615619659424},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1456032395362854},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09919935464859009}],"concepts":[{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.7555055618286133},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7339642643928528},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5866509675979614},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.5354030132293701},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5327790975570679},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5242348313331604},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.482214093208313},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.43511587381362915},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4157133102416992},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37595346570014954},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32844066619873047},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31815797090530396},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16526615619659424},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1456032395362854},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09919935464859009},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C54101563","wikidata":"https://www.wikidata.org/wiki/Q124131","display_name":"Superconductivity","level":2,"score":0.0}],"mesh":[{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1011/48899209/bioinformatics_29_8_1011.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23435067","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23435067","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2625532","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3624810","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:3624810","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3624810","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/1011/48899209/bioinformatics_29_8_1011.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3207356259","display_name":null,"funder_award_id":"2007\u20132013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7546946110","display_name":null,"funder_award_id":"FP/2007-2013)/ERC","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G896728979","display_name":null,"funder_award_id":"FP/2007/2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101072339.pdf","grobid_xml":"https://content.openalex.org/works/W2101072339.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1993038297","https://openalex.org/W1995318306","https://openalex.org/W2003001917","https://openalex.org/W2017777683","https://openalex.org/W2024812560","https://openalex.org/W2036780345","https://openalex.org/W2060425093","https://openalex.org/W2090748603","https://openalex.org/W2099435674","https://openalex.org/W2100945839","https://openalex.org/W2108187446","https://openalex.org/W2111211467","https://openalex.org/W2115888213","https://openalex.org/W2119362018","https://openalex.org/W2137015675","https://openalex.org/W2138369959","https://openalex.org/W2144362290","https://openalex.org/W2147461064","https://openalex.org/W2152688507","https://openalex.org/W2155320525","https://openalex.org/W2157661039","https://openalex.org/W2159957100"],"related_works":["https://openalex.org/W2417800113","https://openalex.org/W4250217664","https://openalex.org/W1967807546","https://openalex.org/W2001721767","https://openalex.org/W2890453921","https://openalex.org/W2028375465","https://openalex.org/W3042188554","https://openalex.org/W2355652392","https://openalex.org/W3158788766","https://openalex.org/W3148913494"],"abstract_inverted_index":{"MOTIVATION:":[0],"Multiple":[1],"sequence":[2,40],"alignments":[3,54,125],"are":[4,19,69,109,126,150],"generally":[5],"reconstructed":[6],"using":[7],"a":[8,13,22,84],"progressive":[9],"approach":[10],"that":[11,48,73,95,106],"follows":[12],"guide-tree.":[14,79,102,118,145],"During":[15],"this":[16],"process,":[17],"gaps":[18,34,52,68,93,108],"introduced":[20],"at":[21,152],"cost":[23],"to":[24,86,135,143],"maximize":[25],"residue":[26],"pairing,":[27],"but":[28,61],"it":[29,62],"is":[30,63,97],"unclear":[31],"whether":[32,67],"inferred":[33,51],"reflect":[35],"actual":[36],"past":[37],"events":[38],"of":[39,50],"insertions":[41],"or":[42],"deletions.":[43],"It":[44],"has":[45],"been":[46],"found":[47],"patterns":[49,113,122],"in":[53,77,100,112,123],"contain":[55],"information":[56,72],"towards":[57],"the":[58,78,88,101,117,140,144],"true":[59],"phylogeny,":[60],"as":[64],"yet":[65],"unknown":[66],"simply":[70],"reflecting":[71],"was":[74],"already":[75,98],"present":[76,99],"RESULTS:":[80],"We":[81],"here":[82],"develop":[83],"framework":[85],"disentangle":[87],"phylogenetic":[89],"signal":[90],"carried":[91],"by":[92],"from":[94],"which":[96],"Our":[103],"results":[104],"indicate":[105],"most":[107,120,141],"incorrectly":[110],"inserted":[111],"that,":[114],"nevertheless,":[115],"follow":[116],"Thus,":[119],"gap":[121],"current":[124],"not":[127],"informative":[128],"per":[129],"se.":[130],"This":[131],"affects":[132],"different":[133],"programs":[134],"various":[136],"degrees,":[137],"PRANK":[138],"being":[139],"sensitive":[142],"SUPPLEMENTARY":[146],"INFORMATION:":[147],"Supplementary":[148],"data":[149],"available":[151],"Bioinformatics":[153],"online.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
