{"id":"https://openalex.org/W4225003079","doi":"https://doi.org/10.1109/tcbb.2022.3170386","title":"SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees","display_name":"SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees","publication_year":2022,"publication_date":"2022-04-26","ids":{"openalex":"https://openalex.org/W4225003079","doi":"https://doi.org/10.1109/tcbb.2022.3170386","pmid":"https://pubmed.ncbi.nlm.nih.gov/35471888"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3170386","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3170386","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/10091711/09763324.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/10091711/09763324.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Eleanor Wedell","orcid":"https://orcid.org/0000-0002-7911-9156"},"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":"Eleanor Wedell","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yirong Cai","orcid":"https://orcid.org/0000-0003-2414-8416"},"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":"Yirong Cai","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":null,"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":false,"raw_author_name":"Tandy Warnow","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":null,"apc_paid":null,"fwci":1.5626,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.8264446,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"20","issue":"2","first_page":"1417","last_page":"1430"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9861999750137329,"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":0.9861999750137329,"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/T10385","display_name":"Plant Diversity and Evolution","score":0.0032999999821186066,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"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/T12359","display_name":"Fern and Epiphyte Biology","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8496999740600586},{"id":"https://openalex.org/keywords/computational-phylogenetics","display_name":"Computational phylogenetics","score":0.6743000149726868},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.616599977016449},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.5820000171661377},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.566100001335144},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.505299985408783},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4936000108718872},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.4496000111103058}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8496999740600586},{"id":"https://openalex.org/C41168302","wikidata":"https://www.wikidata.org/wiki/Q3772859","display_name":"Computational phylogenetics","level":5,"score":0.6743000149726868},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.616599977016449},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.5820000171661377},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.566100001335144},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.505299985408783},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4936000108718872},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4925999939441681},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4496000111103058},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4366999864578247},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4104999899864197},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.3982999920845032},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.37470000982284546},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35989999771118164},{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.3449999988079071},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.32899999618530273},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3203999996185303},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.31540000438690186},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.29019999504089355},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.2872999906539917},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26820001006126404},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.26660001277923584},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25619998574256897},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2556999921798706}],"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","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:10.1109/tcbb.2022.3170386","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3170386","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/10091711/09763324.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35471888","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35471888","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1109/tcbb.2022.3170386","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3170386","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/10091711/09763324.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310230","display_name":"Grainger Foundation","ror":"https://ror.org/0139q7h64"},{"id":"https://openalex.org/F4320315933","display_name":"Siebel Scholars Foundation","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225003079.pdf","grobid_xml":"https://content.openalex.org/works/W4225003079.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1593676244","https://openalex.org/W1748508858","https://openalex.org/W1988925586","https://openalex.org/W2000437405","https://openalex.org/W2031611770","https://openalex.org/W2033900229","https://openalex.org/W2049392778","https://openalex.org/W2056251063","https://openalex.org/W2068187483","https://openalex.org/W2081379565","https://openalex.org/W2084511829","https://openalex.org/W2120878769","https://openalex.org/W2125230147","https://openalex.org/W2150605939","https://openalex.org/W2156542082","https://openalex.org/W2168696662","https://openalex.org/W2949867654","https://openalex.org/W2951358594","https://openalex.org/W2951540755","https://openalex.org/W2952263670","https://openalex.org/W2975848703","https://openalex.org/W2986925300","https://openalex.org/W3005432368","https://openalex.org/W3044581192","https://openalex.org/W3045471380","https://openalex.org/W3109134151","https://openalex.org/W3122087892","https://openalex.org/W3168365712","https://openalex.org/W3205793393","https://openalex.org/W3207897998","https://openalex.org/W6681001129"],"related_works":[],"abstract_inverted_index":{"Phylogenetic":[0,110],"placement,":[1],"the":[2,49,61,65,93,116],"problem":[3],"of":[4,24,118],"placing":[5],"a":[6,10,55,112],"\"query\"":[7],"sequence":[8,51,57],"into":[9],"precomputed":[11],"phylogenetic":[12,157],"\"backbone\"":[13],"tree,":[14],"is":[15],"useful":[16],"for":[17],"constructing":[18],"large":[19,82,98],"trees,":[20,84],"performing":[21],"taxon":[22],"identification":[23],"newly":[25],"obtained":[26],"sequences,":[27],"and":[28,39,46,85,131,151,166],"other":[29],"applications.":[30],"The":[31],"most":[32],"accurate":[33],"current":[34],"methods,":[35],"such":[36],"as":[37],"pplacer":[38],"EPA-ng,":[40],"are":[41,96,168],"based":[42],"on":[43,81,149],"maximum":[44],"likelihood":[45],"require":[47],"that":[48,59,129,147,160],"query":[50],"be":[52],"provided":[53],"within":[54],"multiple":[56],"alignment":[58],"includes":[60],"leaf":[62],"sequences":[63],"in":[64],"backbone":[66,83,94,125,138],"tree.":[67],"This":[68],"approach":[69],"enables":[70],"high":[71],"accuracy":[72,146],"but":[73],"also":[74],"makes":[75],"these":[76,119],"likelihood-based":[77,120],"methods":[78,122,159],"computationally":[79],"intensive":[80],"can":[86],"even":[87],"lead":[88],"to":[89,114,123,136,142,162],"them":[90],"failing":[91],"when":[92],"trees":[95,139],"very":[97],"(e.g.,":[99],"having":[100],"50,000":[101],"or":[102],"more":[103],"leaves).":[104],"We":[105,127],"present":[106],"SCAMPP":[107],"(SCaling":[108],"AlignMent-based":[109],"Placement),":[111],"technique":[113],"extend":[115],"scalability":[117],"placement":[121,158],"ultra-large":[124,137,163],"trees.":[126],"show":[128],"pplacer-SCAMPP":[130,167],"EPA-ng-SCAMPP":[132,165],"both":[133],"scale":[134,161],"well":[135],"(even":[140],"up":[141],"200,000":[143],"leaves),":[144],"with":[145],"improves":[148],"APPLES":[150],"APPLES-2,":[152],"two":[153],"recently":[154],"developed":[155],"fast":[156],"datasets.":[164],"available":[169],"at":[170],"https://github.com/chry04/PLUSplacer.":[171]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2022-04-29T00:00:00"}