{"id":"https://openalex.org/W2123112794","doi":"https://doi.org/10.1186/1471-2105-11-s4-p6","title":"Phylotree \u2013 a toolkit for computing experiments with distance-based methods for genome coevolution","display_name":"Phylotree \u2013 a toolkit for computing experiments with distance-based methods for genome coevolution","publication_year":2010,"publication_date":"2010-07-01","ids":{"openalex":"https://openalex.org/W2123112794","doi":"https://doi.org/10.1186/1471-2105-11-s4-p6","mag":"2123112794"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s4-p6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s4-p6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S4-P6","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S4-P6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077920379","display_name":"Elissaveta Arnaoudova","orcid":null},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elissaveta Arnaoudova","raw_affiliation_strings":["Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA","Department of Computer Science, University of Kentucky Lexington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Department of Computer Science, University of Kentucky Lexington, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058294332","display_name":"Jerzy W. Jaromczyk","orcid":"https://orcid.org/0000-0003-1427-4072"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jerzy W Jaromczyk","raw_affiliation_strings":["Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA","Department of Computer Science, University of Kentucky Lexington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Department of Computer Science, University of Kentucky Lexington, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062751459","display_name":"Neil Moore","orcid":"https://orcid.org/0000-0003-4945-8074"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neil Moore","raw_affiliation_strings":["Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA","Department of Computer Science, University of Kentucky Lexington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Department of Computer Science, University of Kentucky Lexington, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068105637","display_name":"Christopher L. Schardl","orcid":"https://orcid.org/0000-0003-2197-0842"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher L Schardl","raw_affiliation_strings":["Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA","Department of Plant Pathology, University of Kentucky, Lexington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Department of Plant Pathology, University of Kentucky, Lexington, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079338715","display_name":"Ruriko Yoshida","orcid":"https://orcid.org/0000-0003-0995-2553"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruriko Yoshida","raw_affiliation_strings":["Department of Statistics, University of Kentucky, Lexington, KY, 40506, USA","Department of Statistics, University of Kentucky, Lexington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Kentucky, Lexington, KY, 40506, USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Department of Statistics, University of Kentucky, Lexington, USA","institution_ids":["https://openalex.org/I143302722"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058294332"],"corresponding_institution_ids":["https://openalex.org/I143302722"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.14995082,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"S4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9983000159263611,"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"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9925000071525574,"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":0.9915000200271606,"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/coevolution","display_name":"Coevolution","score":0.7101609110832214},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6694040298461914},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6108946800231934},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5743719339370728},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.43370410799980164},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4010656774044037},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2374439835548401},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12449035048484802},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11212676763534546},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.09280511736869812},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08984962105751038}],"concepts":[{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.7101609110832214},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6694040298461914},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6108946800231934},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5743719339370728},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.43370410799980164},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4010656774044037},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2374439835548401},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12449035048484802},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11212676763534546},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.09280511736869812},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08984962105751038}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-s4-p6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s4-p6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S4-P6","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":"pmh:oai:uknowledge.uky.edu:cs_present-1002","is_oa":false,"landing_page_url":"https://uknowledge.uky.edu/cs_present/3","pdf_url":null,"source":{"id":"https://openalex.org/S4306402623","display_name":"UKnowledge (University of Kentucky)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I143302722","host_organization_name":"University of Kentucky","host_organization_lineage":["https://openalex.org/I143302722"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science Presentations","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:8ca3b5bbd0564b99b39b3ed0a9a4b19a","is_oa":true,"landing_page_url":"https://doaj.org/article/8ca3b5bbd0564b99b39b3ed0a9a4b19a","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss Suppl 4, p P6 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3290089","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3290089","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s4-p6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s4-p6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S4-P6","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/G4167810871","display_name":null,"funder_award_id":"0814194","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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123112794.pdf","grobid_xml":"https://content.openalex.org/works/W2123112794.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3144412313","https://openalex.org/W2634235285","https://openalex.org/W2492504662","https://openalex.org/W2122994901","https://openalex.org/W2942642331","https://openalex.org/W200599908","https://openalex.org/W2020991882","https://openalex.org/W2164185151","https://openalex.org/W124046120","https://openalex.org/W3173815060"],"abstract_inverted_index":{"We":[0],"have":[1],"developed":[2],"software":[3],"called":[4],"Phylotree":[5,41],"as":[6,50,52],"a":[7],"toolkit":[8,25],"for":[9,16],"running":[10],"experiments":[11,32,46,72],"to":[12,44,73],"study":[13],"gene":[14],"cophylogenies":[15],"genome":[17],"evolution":[18],"using":[19,47],"distance-based":[20],"methods.":[21],"In":[22],"particular,":[23],"the":[24,34],"has":[26],"been":[27],"instrumental":[28],"in":[29],"conducting":[30],"processing-heavy":[31],"with":[33,65],"new":[35],"\u201cdifference":[36],"of":[37,55],"means\u201d":[38],"statistical":[39],"method.":[40],"was":[42],"used":[43],"run":[45],"simulated":[48],"data":[49,66],"well":[51,56],"biological":[53],"sequences":[54],"known":[57],"host":[58],"and":[59,62,67],"parasite":[60],"species,":[61],"is":[63],"distributed":[64],"configuration":[68],"files":[69],"allowing":[70],"these":[71],"be":[74],"reproduced.":[75]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}