{"id":"https://openalex.org/W2157794452","doi":"https://doi.org/10.1093/bioinformatics/bti289","title":"ProfDist: a tool for the construction of large phylogenetic trees based on profile distances","display_name":"ProfDist: a tool for the construction of large phylogenetic trees based on profile distances","publication_year":2005,"publication_date":"2005-01-27","ids":{"openalex":"https://openalex.org/W2157794452","doi":"https://doi.org/10.1093/bioinformatics/bti289","mag":"2157794452","pmid":"https://pubmed.ncbi.nlm.nih.gov/15677706"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti289","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti289","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/2108/48972725/bioinformatics_21_9_2108.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/2108/48972725/bioinformatics_21_9_2108.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081788489","display_name":"Joachim Friedrich","orcid":null},"institutions":[{"id":"https://openalex.org/I25974101","display_name":"University of W\u00fcrzburg","ror":"https://ror.org/00fbnyb24","country_code":"DE","type":"education","lineage":["https://openalex.org/I25974101"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"J. Friedrich","raw_affiliation_strings":["Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Germany","institution_ids":["https://openalex.org/I25974101"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086202312","display_name":"Thomas Dandekar","orcid":"https://orcid.org/0000-0003-1886-7625"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. Dandekar","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090673895","display_name":"Matthias Wolf","orcid":"https://orcid.org/0000-0003-2004-1806"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Wolf","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5078146941","display_name":"Tobias M\u00fcller","orcid":"https://orcid.org/0000-0003-3035-7070"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. Muller","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081788489"],"corresponding_institution_ids":["https://openalex.org/I25974101"],"apc_list":null,"apc_paid":null,"fwci":0.6279,"has_fulltext":false,"cited_by_count":70,"citation_normalized_percentile":{"value":0.67273153,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"21","issue":"9","first_page":"2108","last_page":"2109"},"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/T10012","display_name":"Genetic diversity and population structure","score":0.9865999817848206,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9423999786376953,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8246543407440186},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5521715879440308},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4092187285423279},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34238213300704956},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22215285897254944},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.16427868604660034},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10775348544120789}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8246543407440186},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5521715879440308},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4092187285423279},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34238213300704956},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22215285897254944},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.16427868604660034},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10775348544120789},{"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti289","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti289","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/2108/48972725/bioinformatics_21_9_2108.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15677706","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15677706","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},{"id":"pmh:oai:publications.rwth-aachen.de:187586","is_oa":false,"landing_page_url":"https://publications.rwth-aachen.de/record/187586","pdf_url":null,"source":{"id":"https://openalex.org/S4306401033","display_name":"RWTH Publications (RWTH Aachen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887968799","host_organization_name":"RWTH Aachen University","host_organization_lineage":["https://openalex.org/I887968799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics 21(9), 2108-2109 (2005). doi:10.1093/bioinformatics/bti289","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti289","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti289","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/2108/48972725/bioinformatics_21_9_2108.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337350","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1045490230","https://openalex.org/W1525734744","https://openalex.org/W1760700012","https://openalex.org/W1996835973","https://openalex.org/W2019032222","https://openalex.org/W2028942402","https://openalex.org/W2030966943","https://openalex.org/W2057081312","https://openalex.org/W2065461553","https://openalex.org/W2071681406","https://openalex.org/W2097706568","https://openalex.org/W2102424972","https://openalex.org/W2120653759","https://openalex.org/W2128599049","https://openalex.org/W2149057166","https://openalex.org/W2150297520","https://openalex.org/W3144631577","https://openalex.org/W4241418020","https://openalex.org/W4254275792"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2362218761","https://openalex.org/W2113708670","https://openalex.org/W2062354928","https://openalex.org/W2088120817"],"abstract_inverted_index":{"SUMMARY:":[0],"ProfDist":[1,55],"is":[2,25,63],"a":[3,26,41,58],"user-friendly":[4],"software":[5],"package":[6],"using":[7],"the":[8],"profile-neighbor-joining":[9],"method":[10],"(PNJ)":[11],"in":[12],"inferring":[13],"phylogenies":[14],"based":[15],"on":[16,19,44],"profile":[17],"distances":[18],"DNA":[20],"or":[21],"RNA":[22],"sequences.":[23],"It":[24],"tool":[27],"for":[28],"reconstructing":[29],"and":[30,37,48,62],"visualizing":[31],"large":[32],"phylogenetic":[33],"trees":[34],"providing":[35],"new":[36],"standard":[38],"features":[39],"with":[40,57],"special":[42],"focus":[43],"time":[45],"efficency,":[46],"robustness":[47],"accuracy.":[49],"AVAILABILITY:":[50],"A":[51],"Windows":[52],"version":[53],"of":[54],"comes":[56],"graphical":[59],"user":[60],"interface":[61],"freely":[64],"available":[65],"at":[66],"http://profdist.bioapps.biozentrum.uni-wuerzburg.de":[67]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":6}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
