{"id":"https://openalex.org/W2013437827","doi":"https://doi.org/10.1371/journal.pcbi.1002495","title":"Simulation of Molecular Data under Diverse Evolutionary Scenarios","display_name":"Simulation of Molecular Data under Diverse Evolutionary Scenarios","publication_year":2012,"publication_date":"2012-05-31","ids":{"openalex":"https://openalex.org/W2013437827","doi":"https://doi.org/10.1371/journal.pcbi.1002495","mag":"2013437827","pmid":"https://pubmed.ncbi.nlm.nih.gov/22693434"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002495","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002495","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002495&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002495&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037761662","display_name":"Miguel Arenas","orcid":"https://orcid.org/0000-0002-0516-2717"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Miguel Arenas","raw_affiliation_strings":["Computational and Molecular Population Genetics Lab-CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. miguel.arenasbusto@iee.unibe.ch","Computational and Molecular Population Genetics Lab (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational and Molecular Population Genetics Lab-CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. miguel.arenasbusto@iee.unibe.ch","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Computational and Molecular Population Genetics Lab (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037761662"],"corresponding_institution_ids":["https://openalex.org/I118564535","https://openalex.org/I12708293"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.6872,"has_fulltext":true,"cited_by_count":70,"citation_normalized_percentile":{"value":0.95327305,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"8","issue":"5","first_page":"e1002495","last_page":"e1002495"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9958999752998352,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4670245945453644},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4641706943511963},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.41514450311660767},{"id":"https://openalex.org/keywords/human-evolutionary-genetics","display_name":"Human evolutionary genetics","score":0.41282832622528076},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.380656898021698},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.20350587368011475},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15274667739868164}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4670245945453644},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4641706943511963},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.41514450311660767},{"id":"https://openalex.org/C167683757","wikidata":"https://www.wikidata.org/wiki/Q5937774","display_name":"Human evolutionary genetics","level":4,"score":0.41282832622528076},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.380656898021698},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.20350587368011475},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15274667739868164},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005060","descriptor_name":"Europe","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005060","descriptor_name":"Europe","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005060","descriptor_name":"Europe","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1002495","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002495","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002495&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:22693434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22693434","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:europepmc.org:2378359","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3364941","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1002495","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002495","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:1bababec30aa433db35f51cedecbc41a","is_oa":true,"landing_page_url":"https://doaj.org/article/1bababec30aa433db35f51cedecbc41a","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":"PLoS Computational Biology, Vol 8, Iss 5, p e1002495 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002495","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002495","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002495&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2013437827.pdf","grobid_xml":"https://content.openalex.org/works/W2013437827.grobid-xml"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W197896231","https://openalex.org/W420957490","https://openalex.org/W1525240758","https://openalex.org/W1541589118","https://openalex.org/W1547520239","https://openalex.org/W1553973053","https://openalex.org/W1585006589","https://openalex.org/W1600815810","https://openalex.org/W1615242748","https://openalex.org/W1867732144","https://openalex.org/W1880845650","https://openalex.org/W1898572544","https://openalex.org/W1967360667","https://openalex.org/W1969761972","https://openalex.org/W1974611538","https://openalex.org/W1984237696","https://openalex.org/W1991599908","https://openalex.org/W1995566547","https://openalex.org/W1999988283","https://openalex.org/W2000519643","https://openalex.org/W2001587667","https://openalex.org/W2019956985","https://openalex.org/W2024398948","https://openalex.org/W2025522412","https://openalex.org/W2026989517","https://openalex.org/W2032643925","https://openalex.org/W2042982067","https://openalex.org/W2043846803","https://openalex.org/W2045239149","https://openalex.org/W2045641296","https://openalex.org/W2046956642","https://openalex.org/W2047378983","https://openalex.org/W2062816199","https://openalex.org/W2063839249","https://openalex.org/W2067423349","https://openalex.org/W2067762850","https://openalex.org/W2079958890","https://openalex.org/W2080426892","https://openalex.org/W2080513977","https://openalex.org/W2093631108","https://openalex.org/W2096697518","https://openalex.org/W2097386339","https://openalex.org/W2100243754","https://openalex.org/W2100874222","https://openalex.org/W2101549247","https://openalex.org/W2101846955","https://openalex.org/W2103546861","https://openalex.org/W2103985888","https://openalex.org/W2104504949","https://openalex.org/W2104690544","https://openalex.org/W2104891575","https://openalex.org/W2105774929","https://openalex.org/W2108675597","https://openalex.org/W2113401798","https://openalex.org/W2116195838","https://openalex.org/W2116209557","https://openalex.org/W2116416291","https://openalex.org/W2116433671","https://openalex.org/W2117804170","https://openalex.org/W2118020384","https://openalex.org/W2119592647","https://openalex.org/W2119632499","https://openalex.org/W2120296271","https://openalex.org/W2120958393","https://openalex.org/W2121167128","https://openalex.org/W2125359798","https://openalex.org/W2127164334","https://openalex.org/W2129016996","https://openalex.org/W2129573652","https://openalex.org/W2130007916","https://openalex.org/W2130824586","https://openalex.org/W2131257659","https://openalex.org/W2133258562","https://openalex.org/W2138877624","https://openalex.org/W2144051643","https://openalex.org/W2144410236","https://openalex.org/W2144658220","https://openalex.org/W2145345672","https://openalex.org/W2147911093","https://openalex.org/W2155294145","https://openalex.org/W2157394513","https://openalex.org/W2157552136","https://openalex.org/W2159866605","https://openalex.org/W2160364329","https://openalex.org/W2164841145","https://openalex.org/W2165036584","https://openalex.org/W2165038845","https://openalex.org/W2165892911","https://openalex.org/W2166734039","https://openalex.org/W2167030304","https://openalex.org/W2171777347","https://openalex.org/W2176261994","https://openalex.org/W2485863807","https://openalex.org/W2885727518","https://openalex.org/W3136389637","https://openalex.org/W3141906900","https://openalex.org/W4229880569","https://openalex.org/W4230357098","https://openalex.org/W4232591682","https://openalex.org/W4243771285","https://openalex.org/W4244406006","https://openalex.org/W4246176452","https://openalex.org/W4285719527","https://openalex.org/W6631548787","https://openalex.org/W6722584863","https://openalex.org/W6753143789","https://openalex.org/W6821112441"],"related_works":["https://openalex.org/W2061542922","https://openalex.org/W2416899523","https://openalex.org/W1984110642","https://openalex.org/W2024428497","https://openalex.org/W2065504586","https://openalex.org/W4319459561","https://openalex.org/W3013401157","https://openalex.org/W2431061071","https://openalex.org/W2165886284","https://openalex.org/W2970921455"],"abstract_inverted_index":{"This":[0],"study":[1,66],"is":[2],"intended":[3],"for":[4,10,44,71],"evolutionary":[5,18],"biologists":[6],"interested":[7],"in":[8,79],"strategies":[9],"the":[11,33],"simulation":[12,27,73],"of":[13,32,58,61],"molecular":[14,80],"data":[15],"under":[16],"diverse":[17],"scenarios.":[19],"It":[20],"begins":[21],"with":[22],"a":[23,56,68],"brief":[24],"background":[25],"on":[26,55],"approaches":[28],"and":[29,50],"describes":[30],"some":[31],"most":[34],"important":[35],"simulators":[36],"developed":[37],"to":[38,75],"date.":[39],"Then,":[40],"several":[41],"practical":[42,69],"examples":[43],"simulating":[45],"particular":[46],"scenarios":[47],"are":[48,53],"presented,":[49],"finally,":[51],"details":[52],"given":[54],"variety":[57],"relevant":[59],"applications":[60],"simulated":[62],"data.":[63],"Overall,":[64],"this":[65],"provides":[67],"guide":[70],"applying":[72],"techniques":[74],"real":[76],"world":[77],"problems":[78],"evolution.":[81]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
