{"id":"https://openalex.org/W2162939356","doi":"https://doi.org/10.1186/1471-2105-12-111","title":"MixtureTree: a program for constructing phylogeny","display_name":"MixtureTree: a program for constructing phylogeny","publication_year":2011,"publication_date":"2011-04-21","ids":{"openalex":"https://openalex.org/W2162939356","doi":"https://doi.org/10.1186/1471-2105-12-111","mag":"2162939356","pmid":"https://pubmed.ncbi.nlm.nih.gov/21615972"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-111","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-111","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-111","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-111","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101497667","display_name":"Shu\u2010Chuan Chen","orcid":"https://orcid.org/0000-0002-3787-2959"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shu-Chuan Chen","raw_affiliation_strings":["School of Mathematical and Statistical Sciences, Arizona State University, Tempe, 85287, USA. scchen@math.asu.edu","School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, 85287, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, Arizona State University, Tempe, 85287, USA. scchen@math.asu.edu","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, 85287, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023032554","display_name":"Michael S. Rosenberg","orcid":"https://orcid.org/0000-0001-7882-2467"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael S Rosenberg","raw_affiliation_strings":["Center for Evolutionary Medicine and Informatics, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Evolutionary Medicine and Informatics, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058460449","display_name":"Bruce G. Lindsay","orcid":"https://orcid.org/0000-0003-3513-911X"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce G Lindsay","raw_affiliation_strings":["Department of Statistics, Pennsylvania State University, University Park, PA, 16802, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Pennsylvania State University, University Park, PA, 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101497667"],"corresponding_institution_ids":["https://openalex.org/I55732556"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9125,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.83543515,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"1","first_page":"111","last_page":"111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.26100000739097595,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.26100000739097595,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.21330000460147858,"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":0.13670000433921814,"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/computer-science","display_name":"Computer science","score":0.6283806562423706},{"id":"https://openalex.org/keywords/expectation\u2013maximization-algorithm","display_name":"Expectation\u2013maximization algorithm","score":0.5353413820266724},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.5043786764144897},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.44676223397254944},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.43894678354263306},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"Maximum parsimony","score":0.4294899106025696},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4182981848716736},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41695427894592285},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.4107182025909424},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3864341974258423},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35585910081863403},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.35129237174987793},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22311905026435852},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17693117260932922},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15306007862091064},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12172582745552063},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11090362071990967}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6283806562423706},{"id":"https://openalex.org/C182081679","wikidata":"https://www.wikidata.org/wiki/Q1275153","display_name":"Expectation\u2013maximization algorithm","level":3,"score":0.5353413820266724},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.5043786764144897},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.44676223397254944},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.43894678354263306},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.4294899106025696},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4182981848716736},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41695427894592285},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.4107182025909424},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3864341974258423},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35585910081863403},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.35129237174987793},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22311905026435852},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17693117260932922},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15306007862091064},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12172582745552063},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11090362071990967},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"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/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"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":"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":"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-12-111","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-111","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-111","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21615972","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21615972","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:64a4a884ceca462e84bbe1127f91c781","is_oa":false,"landing_page_url":"https://doaj.org/article/64a4a884ceca462e84bbe1127f91c781","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 111 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3102041","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3102041","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-111","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-111","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-111","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1400301709","display_name":"Collaborative Research: Statistical Methods and Algorithms for Genomic Data","funder_award_id":"0714839","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3032134887","display_name":"Collaborative Research: Statistical Methods and Algorithms for Genomic Data","funder_award_id":"0714949","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"},{"id":"https://openalex.org/F4320311041","display_name":"National Center for Theoretical Sciences","ror":"https://ror.org/02mfp0b67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162939356.pdf","grobid_xml":"https://content.openalex.org/works/W2162939356.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1546639740","https://openalex.org/W2015800458","https://openalex.org/W2035109830","https://openalex.org/W2048945600","https://openalex.org/W2049343897","https://openalex.org/W2060425093","https://openalex.org/W2110899053","https://openalex.org/W2121160345","https://openalex.org/W2134599124","https://openalex.org/W2136287174","https://openalex.org/W2141913814","https://openalex.org/W2146058063","https://openalex.org/W2161457086","https://openalex.org/W2289587704","https://openalex.org/W2796384310","https://openalex.org/W3199943451","https://openalex.org/W3217097258","https://openalex.org/W4233815609","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1978153144","https://openalex.org/W4244797807","https://openalex.org/W2036614038","https://openalex.org/W102848802","https://openalex.org/W4255917406","https://openalex.org/W2982058819","https://openalex.org/W29503807","https://openalex.org/W2130734797","https://openalex.org/W2172249169","https://openalex.org/W3176361882"],"abstract_inverted_index":{"BACKGROUND:":[0],"MixtureTree":[1,54],"v1.0":[2],"is":[3,59,82],"a":[4,46,60],"Linux":[5,61],"based":[6,15,62],"program":[7,43,55],"(written":[8],"in":[9,57],"C++)":[10],"which":[11],"implements":[12,45],"an":[13],"algorithm":[14,36,81],"on":[16],"mixture":[17,35,80,104],"models":[18],"for":[19,107],"reconstructing":[20],"phylogeny":[21],"from":[22],"binary":[23],"sequence":[24],"data,":[25],"such":[26,89],"as":[27,90],"single-nucleotide":[28],"polymorphisms":[29],"(SNPs).":[30],"In":[31],"addition":[32],"to":[33],"the":[34,42,79,103,122],"with":[37,49],"three":[38],"different":[39],"optimization":[40],"options,":[41],"also":[44],"bootstrap":[47],"procedure":[48],"majority-rule":[50],"consensus.":[51],"RESULTS:":[52],"The":[53,64,76,100],"written":[56],"C++":[58],"package.":[63],"User's":[65],"Guide":[66],"and":[67,96],"source":[68],"codes":[69],"will":[70],"be":[71,112],"available":[72],"at":[73],"http://math.asu.edu/~scchen/MixtureTree.html":[74],"CONCLUSIONS:":[75],"efficiency":[77],"of":[78,102,121],"relatively":[83],"higher":[84],"than":[85],"some":[86],"classical":[87],"methods,":[88],"Neighbor-Joining":[91],"method,":[92],"Maximum":[93,97],"Parsimony":[94],"method":[95],"Likelihood":[98],"method.":[99],"shortcoming":[101],"tree":[105],"algorithms,":[106],"example":[108],"timing":[109],"consuming,":[110],"can":[111],"improved":[113],"by":[114],"implementing":[115],"other":[116],"revised":[117],"Expectation-Maximization(EM)":[118],"algorithms":[119],"instead":[120],"traditional":[123],"EM":[124],"algorithm.":[125]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
