{"id":"https://openalex.org/W3185594128","doi":"https://doi.org/10.1093/bioinformatics/btab555","title":"Accurate large-scale phylogeny-aware alignment using BAli-Phy","display_name":"Accurate large-scale phylogeny-aware alignment using BAli-Phy","publication_year":2021,"publication_date":"2021-07-27","ids":{"openalex":"https://openalex.org/W3185594128","doi":"https://doi.org/10.1093/bioinformatics/btab555","mag":"3185594128","pmid":"https://pubmed.ncbi.nlm.nih.gov/34320635"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab555","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab555","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/A5111921762","display_name":"Maya R. Gupta","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maya Gupta","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014969856","display_name":"Paul Zaharias","orcid":"https://orcid.org/0000-0003-3550-2636"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Zaharias","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032411541","display_name":"Tandy Warnow","orcid":"https://orcid.org/0000-0001-7717-3514"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tandy Warnow","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032411541"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3218,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.55750889,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"24","first_page":"4677","last_page":"4683"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9857000112533569,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9814000129699707,"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/phylogenetics","display_name":"Phylogenetics","score":0.651308536529541},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.6367266178131104},{"id":"https://openalex.org/keywords/phy","display_name":"PHY","score":0.6164080500602722},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5951897501945496},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3286575675010681},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2616279721260071},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.20895862579345703},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.17315709590911865},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11767572164535522},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.0692179799079895}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.651308536529541},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.6367266178131104},{"id":"https://openalex.org/C41918916","wikidata":"https://www.wikidata.org/wiki/Q192727","display_name":"PHY","level":4,"score":0.6164080500602722},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5951897501945496},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3286575675010681},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2616279721260071},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.20895862579345703},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.17315709590911865},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11767572164535522},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0692179799079895},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C19247436","wikidata":"https://www.wikidata.org/wiki/Q192727","display_name":"Physical layer","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007214","descriptor_name":"Indonesia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007214","descriptor_name":"Indonesia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007214","descriptor_name":"Indonesia","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab555","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab555","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:34320635","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34320635","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6756578768","display_name":null,"funder_award_id":"ABI-1458652","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1593676244","https://openalex.org/W1748508858","https://openalex.org/W1972745976","https://openalex.org/W2007668764","https://openalex.org/W2017777683","https://openalex.org/W2031611770","https://openalex.org/W2056251063","https://openalex.org/W2060425093","https://openalex.org/W2078802219","https://openalex.org/W2101072339","https://openalex.org/W2111211467","https://openalex.org/W2127322768","https://openalex.org/W2127520112","https://openalex.org/W2132926880","https://openalex.org/W2138317639","https://openalex.org/W2140872496","https://openalex.org/W2141052558","https://openalex.org/W2144362290","https://openalex.org/W2144775551","https://openalex.org/W2148450265","https://openalex.org/W2154099008","https://openalex.org/W2154598603","https://openalex.org/W2157451851","https://openalex.org/W2157552136","https://openalex.org/W2159235552","https://openalex.org/W2159638180","https://openalex.org/W2160378127","https://openalex.org/W2169602699","https://openalex.org/W2174364811","https://openalex.org/W2267533067","https://openalex.org/W2896071897","https://openalex.org/W2982461819","https://openalex.org/W2991142785","https://openalex.org/W3005235420","https://openalex.org/W3044581192","https://openalex.org/W3109134151","https://openalex.org/W3135507857","https://openalex.org/W4245668478","https://openalex.org/W6681367416"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4283023968","https://openalex.org/W1964667553","https://openalex.org/W2390471376","https://openalex.org/W2001476941","https://openalex.org/W2530058746","https://openalex.org/W1487710470","https://openalex.org/W1939593940","https://openalex.org/W1483545079","https://openalex.org/W2109048287"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-02-27T16:54:17.756197","created_date":"2025-10-10T00:00:00"}
