{"id":"https://openalex.org/W2144454528","doi":"https://doi.org/10.1186/1748-7188-5-16","title":"Jane: a new tool for the cophylogeny reconstruction problem","display_name":"Jane: a new tool for the cophylogeny reconstruction problem","publication_year":2010,"publication_date":"2010-02-03","ids":{"openalex":"https://openalex.org/W2144454528","doi":"https://doi.org/10.1186/1748-7188-5-16","mag":"2144454528","pmid":"https://pubmed.ncbi.nlm.nih.gov/20181081"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-5-16","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-16","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-16","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-16","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059743010","display_name":"Chris Conow","orcid":null},"institutions":[{"id":"https://openalex.org/I98947143","display_name":"California State Polytechnic University","ror":"https://ror.org/05by5hm18","country_code":"US","type":"education","lineage":["https://openalex.org/I98947143"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Conow","raw_affiliation_strings":["Department of Computer Science, California State Polytechnic University, Pomona, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, California State Polytechnic University, Pomona, CA, USA","institution_ids":["https://openalex.org/I98947143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045392848","display_name":"Daniel C. Fielder","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Fielder","raw_affiliation_strings":["Department of Computer Science, Harvey Mudd College, Claremont, CA, USA","Dept. of Computer Science, Harvey Mudd College, Claremont, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]},{"raw_affiliation_string":"Dept. of Computer Science, Harvey Mudd College, Claremont, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045421827","display_name":"Yaniv Ovadia","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yaniv Ovadia","raw_affiliation_strings":["Department of Computer Science, Harvey Mudd College, Claremont, CA, USA","Dept. of Computer Science, Harvey Mudd College, Claremont, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]},{"raw_affiliation_string":"Dept. of Computer Science, Harvey Mudd College, Claremont, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081839833","display_name":"Ran Libeskind-Hadas","orcid":"https://orcid.org/0000-0001-9120-1948"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ran Libeskind-Hadas","raw_affiliation_strings":["Department of Computer Science, Harvey Mudd College, Claremont, CA, USA","Dept. of Computer Science, Harvey Mudd College, Claremont, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]},{"raw_affiliation_string":"Dept. of Computer Science, Harvey Mudd College, Claremont, USA","institution_ids":["https://openalex.org/I133543626"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5081839833"],"corresponding_institution_ids":["https://openalex.org/I133543626"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":23.9842,"has_fulltext":true,"cited_by_count":412,"citation_normalized_percentile":{"value":0.99604987,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"5","issue":"1","first_page":"16","last_page":"16"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12637","display_name":"Scarabaeidae Beetle Taxonomy and Biogeography","score":0.15299999713897705,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12637","display_name":"Scarabaeidae Beetle Taxonomy and Biogeography","score":0.15299999713897705,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12132","display_name":"Hymenoptera taxonomy and phylogeny","score":0.07370000332593918,"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/T11179","display_name":"Nematode management and characterization studies","score":0.06549999862909317,"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/computer-science","display_name":"Computer science","score":0.7185652852058411},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.6727265119552612},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6282033920288086},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4827806055545807},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4814131259918213},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4542127847671509},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44422993063926697},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.4189497232437134},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.36559468507766724},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3373459279537201},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2512172758579254},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.19484105706214905},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1781148612499237},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12216469645500183}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7185652852058411},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.6727265119552612},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6282033920288086},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4827806055545807},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4814131259918213},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4542127847671509},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44422993063926697},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.4189497232437134},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36559468507766724},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3373459279537201},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2512172758579254},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.19484105706214905},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1781148612499237},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12216469645500183},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1748-7188-5-16","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-16","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-16","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:20181081","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20181081","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:scholarship.claremont.edu:hmc_fac_pub-1905","is_oa":false,"landing_page_url":"https://scholarship.claremont.edu/hmc_fac_pub/901","pdf_url":null,"source":{"id":"https://openalex.org/S4306401604","display_name":"Scholarship @ Claremont (The Claremont Colleges)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I872248612","host_organization_name":"Claremont Colleges","host_organization_lineage":["https://openalex.org/I872248612"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"All HMC Faculty Publications and Research","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:764fa3fc03654c5aa5c7c465e325ca18","is_oa":true,"landing_page_url":"https://doaj.org/article/764fa3fc03654c5aa5c7c465e325ca18","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":"Algorithms for Molecular Biology, Vol 5, Iss 1, p 16 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2830923","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2830923","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-5-16","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-16","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-16","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3810107827","display_name":"REU Site: REU Site in Computer Systems","funder_award_id":"0753306","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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144454528.pdf","grobid_xml":"https://content.openalex.org/works/W2144454528.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1970909551","https://openalex.org/W1986876977","https://openalex.org/W1992274351","https://openalex.org/W1996156981","https://openalex.org/W2008252897","https://openalex.org/W2034492097","https://openalex.org/W2090867176","https://openalex.org/W2117000771","https://openalex.org/W2118960257","https://openalex.org/W2119670789","https://openalex.org/W2122000456","https://openalex.org/W2126338599","https://openalex.org/W2128520958","https://openalex.org/W2144619586","https://openalex.org/W2146683389","https://openalex.org/W2165843346","https://openalex.org/W2166782990","https://openalex.org/W2994030436"],"related_works":["https://openalex.org/W2022968056","https://openalex.org/W3180179400","https://openalex.org/W2118366689","https://openalex.org/W2154998455","https://openalex.org/W2116888309","https://openalex.org/W1649706580","https://openalex.org/W2477652530","https://openalex.org/W2039055059","https://openalex.org/W3195608031","https://openalex.org/W2381088774"],"abstract_inverted_index":{"BACKGROUND:":[0],"This":[1,21],"paper":[2],"describes":[3],"the":[4,16,77,125,134,141,158,179,187,191,222],"theory":[5],"and":[6,29,36,38,43,60,74,76,111,136,148,161,210,228],"implementation":[7],"of":[8,18,27,34,41,50,53,120,168,217,224],"a":[9,95,104,173,199],"new":[10,78],"software":[11,67,92],"tool,":[12],"called":[13],"Jane,":[14],"for":[15,69,116,163,202],"study":[17],"historical":[19],"associations.":[20],"problem":[22,47,71],"arises":[23],"in":[24,101,157,221],"parasitology":[25],"(associations":[26,33,40],"hosts":[28],"parasites),":[30],"molecular":[31,226],"systematics":[32],"orderings":[35],"genes),":[37],"biogeography":[39],"regions":[42,156],"orderings).":[44],"The":[45,90,122],"underlying":[46],"is":[48,195,212],"that":[49,85,177],"reconciling":[51],"pairs":[52,119,167],"trees":[54],"subject":[55],"to":[56,107,127,181,186,197,215,219],"biologically":[57],"plausible":[58],"events":[59],"costs":[61,153,162],"associated":[62],"with":[63,103,184],"these":[64],"events.":[65],"Existing":[66],"tools":[68,209],"this":[70],"have":[72],"strengths":[73],"limitations,":[75],"Jane":[79,91,170,194],"tool":[80,93,123,201],"described":[81],"here":[82],"provides":[83,172],"functionality":[84,206],"complements":[86,207],"existing":[87,208],"tools.":[88],"RESULTS:":[89],"uses":[94],"polynomial":[96],"time":[97],"dynamic":[98],"programming":[99],"algorithm":[100,106],"conjunction":[102],"genetic":[105],"find":[108],"very":[109],"good,":[110],"often":[112],"optimal,":[113],"solutions":[114,188],"even":[115],"relatively":[117],"large":[118],"trees.":[121,138],"allows":[124,178],"user":[126,142,175,180],"provide":[128],"rich":[129],"timing":[130],"information":[131],"on":[132],"both":[133],"host":[135,145,151,159,164],"parasite":[137],"In":[139],"addition":[140],"can":[143],"limit":[144],"switch":[146,152],"distance":[147],"specify":[149],"multiple":[150],"by":[154,190],"specifying":[155],"tree":[160],"switches":[165],"between":[166],"regions.":[169],"also":[171],"graphical":[174],"interface":[176],"interactively":[182],"experiment":[183],"modifications":[185],"found":[189],"program.":[192],"CONCLUSIONS:":[193],"shown":[196],"be":[198,216],"useful":[200],"cophylogenetic":[203],"reconstruction.":[204],"Its":[205],"it":[211],"therefore":[213],"likely":[214],"use":[218],"researchers":[220],"areas":[223],"parasitology,":[225],"systematics,":[227],"biogeography.":[229]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":35},{"year":2019,"cited_by_count":37},{"year":2018,"cited_by_count":28},{"year":2017,"cited_by_count":40},{"year":2016,"cited_by_count":34},{"year":2015,"cited_by_count":21},{"year":2014,"cited_by_count":21},{"year":2013,"cited_by_count":24},{"year":2012,"cited_by_count":16}],"updated_date":"2026-07-05T07:55:05.734416","created_date":"2025-10-10T00:00:00"}
