{"id":"https://openalex.org/W2193289889","doi":"https://doi.org/10.3390/computation3040701","title":"Exact Likelihood Calculation under the Infinite Sites Model","display_name":"Exact Likelihood Calculation under the Infinite Sites Model","publication_year":2015,"publication_date":"2015-12-11","ids":{"openalex":"https://openalex.org/W2193289889","doi":"https://doi.org/10.3390/computation3040701","mag":"2193289889"},"language":"en","primary_location":{"id":"doi:10.3390/computation3040701","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3040701","pdf_url":"https://www.mdpi.com/2079-3197/3/4/701/pdf?version=1450177201","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2079-3197/3/4/701/pdf?version=1450177201","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067006328","display_name":"Muhammad Faisal","orcid":"https://orcid.org/0000-0003-4885-4251"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I139894009","display_name":"University of Bradford","ror":"https://ror.org/00vs8d940","country_code":"GB","type":"education","lineage":["https://openalex.org/I139894009"]},{"id":"https://openalex.org/I4210166758","display_name":"Bradford Teaching Hospitals NHS Foundation Trust","ror":"https://ror.org/05gekvn04","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210166758"]}],"countries":["AT","GB"],"is_corresponding":false,"raw_author_name":"Muhammad Faisal","raw_affiliation_strings":["Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford BD96RJ, UK","Department of Statistics and Operations Research, University of Vienna, 1090 Vienna, Austria","Faculty of Health Studies, University of Bradford, Bradford BD71DP, UK"],"affiliations":[{"raw_affiliation_string":"Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford BD96RJ, UK","institution_ids":["https://openalex.org/I4210166758"]},{"raw_affiliation_string":"Department of Statistics and Operations Research, University of Vienna, 1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Faculty of Health Studies, University of Bradford, Bradford BD71DP, UK","institution_ids":["https://openalex.org/I139894009"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011496906","display_name":"Andreas Futschik","orcid":"https://orcid.org/0000-0002-7980-0304"},"institutions":[{"id":"https://openalex.org/I121883995","display_name":"Johannes Kepler University of Linz","ror":"https://ror.org/052r2xn60","country_code":"AT","type":"education","lineage":["https://openalex.org/I121883995"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Andreas Futschik","raw_affiliation_strings":["Institute of Applied Statistics, Johannes Kepler University Linz, 4040 Linz, Austria"],"affiliations":[{"raw_affiliation_string":"Institute of Applied Statistics, Johannes Kepler University Linz, 4040 Linz, Austria","institution_ids":["https://openalex.org/I121883995"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023097867","display_name":"Claus Vogl","orcid":"https://orcid.org/0000-0002-3996-7863"},"institutions":[{"id":"https://openalex.org/I150540706","display_name":"University of Veterinary Medicine Vienna","ror":"https://ror.org/01w6qp003","country_code":"AT","type":"education","lineage":["https://openalex.org/I150540706"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Claus Vogl","raw_affiliation_strings":["Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterin\u00e4rplatz 1, 1210 Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterin\u00e4rplatz 1, 1210 Vienna, Austria","institution_ids":["https://openalex.org/I150540706"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023097867"],"corresponding_institution_ids":["https://openalex.org/I150540706"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.2392,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.67388753,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"3","issue":"4","first_page":"701","last_page":"713"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9979000091552734,"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":0.9979000091552734,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9973999857902527,"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/T11152","display_name":"Stochastic processes and statistical mechanics","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2610","display_name":"Mathematical Physics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/coalescent-theory","display_name":"Coalescent theory","score":0.8430659174919128},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5414896011352539},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.5380806922912598},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.5105210542678833},{"id":"https://openalex.org/keywords/mutation-rate","display_name":"Mutation rate","score":0.5059725642204285},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.49510326981544495},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4908478856086731},{"id":"https://openalex.org/keywords/constant","display_name":"Constant (computer programming)","score":0.4827991724014282},{"id":"https://openalex.org/keywords/population-size","display_name":"Population size","score":0.47638291120529175},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.4572522044181824},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4498898983001709},{"id":"https://openalex.org/keywords/effective-population-size","display_name":"Effective population size","score":0.4244332015514374},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.282758891582489},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.27057865262031555},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.248343825340271},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1854112148284912},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.13182836771011353},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10614371299743652},{"id":"https://openalex.org/keywords/genetic-variation","display_name":"Genetic variation","score":0.08718293905258179}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.8430659174919128},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5414896011352539},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5380806922912598},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.5105210542678833},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.5059725642204285},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.49510326981544495},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4908478856086731},{"id":"https://openalex.org/C2777027219","wikidata":"https://www.wikidata.org/wiki/Q1284190","display_name":"Constant (computer programming)","level":2,"score":0.4827991724014282},{"id":"https://openalex.org/C169733012","wikidata":"https://www.wikidata.org/wiki/Q1613416","display_name":"Population size","level":3,"score":0.47638291120529175},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.4572522044181824},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4498898983001709},{"id":"https://openalex.org/C3641667","wikidata":"https://www.wikidata.org/wiki/Q1295959","display_name":"Effective population size","level":4,"score":0.4244332015514374},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.282758891582489},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27057865262031555},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.248343825340271},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1854112148284912},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.13182836771011353},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10614371299743652},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.08718293905258179},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/computation3040701","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3040701","pdf_url":"https://www.mdpi.com/2079-3197/3/4/701/pdf?version=1450177201","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:e40c459bbee9474da4aa96d5c3677cac","is_oa":true,"landing_page_url":"https://doaj.org/article/e40c459bbee9474da4aa96d5c3677cac","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computation, Vol 3, Iss 4, Pp 701-713 (2015)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2079-3197/3/4/701/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/computation3040701","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Computation","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/computation3040701","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3040701","pdf_url":"https://www.mdpi.com/2079-3197/3/4/701/pdf?version=1450177201","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6299999952316284,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2193289889.pdf","grobid_xml":"https://content.openalex.org/works/W2193289889.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1503883746","https://openalex.org/W1519103070","https://openalex.org/W1525240758","https://openalex.org/W1980674207","https://openalex.org/W2040640649","https://openalex.org/W2110221181","https://openalex.org/W2117453125","https://openalex.org/W2130333286","https://openalex.org/W2130362098","https://openalex.org/W2134599124","https://openalex.org/W2147476214","https://openalex.org/W3004157836","https://openalex.org/W4388322114"],"related_works":["https://openalex.org/W2898028641","https://openalex.org/W2103667393","https://openalex.org/W2953115706","https://openalex.org/W3042201913","https://openalex.org/W2273451097","https://openalex.org/W2961040797","https://openalex.org/W2040155323","https://openalex.org/W3013529535","https://openalex.org/W3091872977","https://openalex.org/W2756193737"],"abstract_inverted_index":{"A":[0],"key":[1],"parameter":[2,73],"in":[3,42,104,112,129,170,207],"population":[4,23,43],"genetics":[5],"is":[6,19,27,39,60,99,122,137,149,199],"the":[7,20,28,66,97,102,113,130,134,150,179,191,200,208],"scaled":[8],"mutation":[9,29],"rate":[10,30],"\u03b8":[11,58,74,143,155,171,183],"=":[12],"4":[13],"N":[14,18],"\u03bc":[15,26],",":[16,146,159],"where":[17,147],"effective":[21],"haploid":[22],"size":[24],"and":[25,89,106,127,181],"per":[31,33],"haplotype":[32],"generation.":[34],"While":[35],"exact":[36],"likelihood":[37,56,206],"inference":[38],"notoriously":[40],"difficult":[41],"genetics,":[44],"we":[45,160],"propose":[46],"a":[47,52,162,167,205],"novel":[48],"approach":[49,103],"to":[50,101,185],"compute":[51],"first":[53,201],"order":[54],"accurate":[55,202],"of":[57,87,193,204],"that":[59,121],"based":[61,123],"on":[62,124],"dynamic":[63],"programming":[64],"under":[65],"infinite":[67,209],"sites":[68,210],"model":[69,165,211],"without":[70],"recombination.":[71],"The":[72],"may":[75],"be":[76,186],"either":[77],"constant,":[78],"i.e.,":[79],"time-independent,":[80],"or":[81],"time-dependent,":[82],"which":[83],"allows":[84],"for":[85],"changes":[86],"demography":[88],"deviations":[90],"from":[91],"neutral":[92],"equilibrium.":[93],"For":[94,153],"time-independent":[95],"\u03b8,":[96],"performance":[98],"compared":[100],"Griffiths":[105],"Tavar\u00e9\u2019s":[107],"work":[108],"\u201cSimulating":[109],"Probability":[110],"Distributions":[111],"Coalescent\u201d":[114],"(Theor.":[115],"Popul.":[116],"Biol.":[117],"1994,":[118],"46,":[119],"131\u2013159)":[120],"importance":[125],"sampling":[126],"implemented":[128],"\u201cgenetree\u201d":[131],"program.":[132],"Roughly,":[133],"proposed":[135],"method":[136],"computationally":[138],"fast":[139],"when":[140],"n":[141,148],"\u00d7":[142],"<":[144],"100":[145],"sample":[151],"size.":[152],"time-dependent":[154],"(":[156,172],"t":[157,173],")":[158,174],"analyze":[161],"simple":[163],"demographic":[164],"with":[166,212],"single":[168],"change":[169],".":[175],"In":[176],"this":[177,198],"case,":[178],"ancestral":[180],"current":[182],"need":[184],"estimated,":[187],"as":[188,190],"well":[189],"time":[192],"change.":[194],"To":[195],"our":[196],"knowledge,":[197],"computation":[203],"non-equilibrium":[213],"demography.":[214]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}