{"id":"https://openalex.org/W2155604079","doi":"https://doi.org/10.1145/2147805.2147868","title":"TreeLign","display_name":"TreeLign","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2155604079","doi":"https://doi.org/10.1145/2147805.2147868","mag":"2155604079"},"language":"en","primary_location":{"id":"doi:10.1145/2147805.2147868","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147868","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://stars.library.ucf.edu/scopus2010/2221","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101460607","display_name":"Yuan Li","orcid":"https://orcid.org/0000-0001-7735-9255"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuan Li","raw_affiliation_strings":["University of Central Florida, Orlando, FL"],"affiliations":[{"raw_affiliation_string":"University of Central Florida, Orlando, FL","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111911477","display_name":"Aaron L. Halpern","orcid":null},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron L. Halpern","raw_affiliation_strings":["J. Craig Venter Institute, Rockville, MD"],"affiliations":[{"raw_affiliation_string":"J. Craig Venter Institute, Rockville, MD","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100768909","display_name":"Shaojie Zhang","orcid":"https://orcid.org/0000-0002-4051-5549"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaojie Zhang","raw_affiliation_strings":["University of Central Florida, Orlando, FL"],"affiliations":[{"raw_affiliation_string":"University of Central Florida, Orlando, FL","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101460607"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13581766,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"155","issue":null,"first_page":"451","last_page":"456"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9927999973297119,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8189154863357544},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6722211837768555},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.643805980682373},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5826443433761597},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5107095241546631},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5101168751716614},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"Maximum parsimony","score":0.4732811152935028},{"id":"https://openalex.org/keywords/tree-rearrangement","display_name":"Tree rearrangement","score":0.4665731191635132},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4641578793525696},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43462392687797546},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3789437711238861},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3750249445438385},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20274072885513306},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18382346630096436},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.17143112421035767},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.0714648962020874}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8189154863357544},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6722211837768555},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.643805980682373},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5826443433761597},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5107095241546631},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5101168751716614},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.4732811152935028},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.4665731191635132},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4641578793525696},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43462392687797546},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3789437711238861},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3750249445438385},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20274072885513306},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18382346630096436},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.17143112421035767},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0714648962020874},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2147805.2147868","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147868","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:stars.library.ucf.edu:scopus2010-3220","is_oa":true,"landing_page_url":"https://stars.library.ucf.edu/scopus2010/2221","pdf_url":null,"source":{"id":"https://openalex.org/S4210172555","display_name":"Journal of International Crisis and Risk Communication Research","issn_l":"2576-0017","issn":["2576-0017","2576-0025"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus Export 2010-2014","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:stars.library.ucf.edu:scopus2010-3220","is_oa":true,"landing_page_url":"https://stars.library.ucf.edu/scopus2010/2221","pdf_url":null,"source":{"id":"https://openalex.org/S4210172555","display_name":"Journal of International Crisis and Risk Communication Research","issn_l":"2576-0017","issn":["2576-0017","2576-0025"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus Export 2010-2014","raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1963957860","https://openalex.org/W1988925586","https://openalex.org/W1990061958","https://openalex.org/W1990722492","https://openalex.org/W2000437405","https://openalex.org/W2000795465","https://openalex.org/W2002638840","https://openalex.org/W2009570821","https://openalex.org/W2030154486","https://openalex.org/W2041076979","https://openalex.org/W2055344823","https://openalex.org/W2068687524","https://openalex.org/W2075623226","https://openalex.org/W2079706758","https://openalex.org/W2084251919","https://openalex.org/W2091922579","https://openalex.org/W2095581275","https://openalex.org/W2097020631","https://openalex.org/W2111775329","https://openalex.org/W2113601822","https://openalex.org/W2119428521","https://openalex.org/W2124637227","https://openalex.org/W2126809954","https://openalex.org/W2139436782","https://openalex.org/W2150605939","https://openalex.org/W2152885278","https://openalex.org/W2154969423","https://openalex.org/W2155806125","https://openalex.org/W2168696662","https://openalex.org/W2170996473","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2520823390","https://openalex.org/W4300265711","https://openalex.org/W2963820820","https://openalex.org/W2120975787","https://openalex.org/W2362218761","https://openalex.org/W1492943375","https://openalex.org/W4389053046","https://openalex.org/W2370337517","https://openalex.org/W4401807688","https://openalex.org/W2113708670"],"abstract_inverted_index":{"Phylogenetic":[0],"assignment":[1],"of":[2,19,91,126,136,153,165,175,179],"16s":[3],"rRNA":[4,146],"has":[5,25],"been":[6],"frequently":[7],"used":[8],"for":[9,53,76,99],"taxonomic":[10,30],"classification.":[11],"Recently,":[12],"high-throughput":[13],"sequencing,":[14],"especially":[15],"in":[16,55,124,168],"the":[17,95,132,150,158,163,172,176,182,185],"context":[18],"environmental":[20],"or":[21,46],"metagenomic":[22],"sequencing":[23],"projects,":[24],"made":[26],"fast":[27],"and":[28,44,48,69,73,84,110,116,134,142],"accurate":[29,49],"classification":[31,36],"an":[32,85],"important":[33],"goal.":[34],"Existing":[35],"methods":[37],"are":[38,121,167],"either":[39],"fast,":[40],"but":[41,50,201],"too":[42,51],"coarse-grained":[43],"inaccurate":[45],"fine-grained":[47],"slow":[52],"use":[54],"practice.":[56],"In":[57],"this":[58],"paper,":[59],"we":[60],"propose":[61],"a":[62,80,113,117,140,143],"new":[63,114,118],"computational":[64,205],"method,":[65],"TreeLign,":[66],"to":[67,106],"rapidly":[68],"accurately":[70],"conduct":[71],"alignment":[72,119],"phylogenetic":[74,82,173],"assignments":[75,164],"novel":[77],"sequences,":[78],"given":[79],"reference":[81,96],"tree":[83,115,174],"alignment.":[86],"TreeLign":[87,137,166,190],"first":[88],"constructs":[89],"profiles":[90],"every":[92,107],"branch":[93],"on":[94,138,157,184],"tree,":[97],"then,":[98],"each":[100],"query":[101],"sequence,":[102],"tries":[103],"assigning":[104],"it":[105],"possible":[108],"branch,":[109],"finally":[111],"obtains":[112],"which":[120],"jointly":[122],"optimal":[123],"terms":[125],"Maximum":[127],"Parsimony":[128],"(MP).":[129],"We":[130],"tested":[131],"accuracy":[133,193],"robustness":[135],"both":[139],"large":[141,159],"small":[144,186],"16S":[145],"dataset":[147,160,187],"extracted":[148],"from":[149],"core":[151,177],"set":[152,178],"GreenGenes.":[154,180],"The":[155],"results":[156,183],"show":[161,188],"that":[162,189],"general":[169],"consistent":[170],"with":[171,195],"And,":[181],"achieves":[191],"comparable":[192],"compared":[194],"existing":[196],"maximum":[197],"likelihood":[198],"based":[199],"methods,":[200],"requires":[202],"much":[203],"less":[204],"time.":[206]},"counts_by_year":[],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2016-06-24T00:00:00"}
