{"id":"https://openalex.org/W1976923174","doi":"https://doi.org/10.3390/computation3020177","title":"A Guide to Phylogenetic Reconstruction Using Heterogeneous Models\u2014A Case Study from the Root of the Placental Mammal Tree","display_name":"A Guide to Phylogenetic Reconstruction Using Heterogeneous Models\u2014A Case Study from the Root of the Placental Mammal Tree","publication_year":2015,"publication_date":"2015-04-15","ids":{"openalex":"https://openalex.org/W1976923174","doi":"https://doi.org/10.3390/computation3020177","mag":"1976923174"},"language":"en","primary_location":{"id":"doi:10.3390/computation3020177","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3020177","pdf_url":"https://www.mdpi.com/2079-3197/3/2/177/pdf?version=1429086192","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/2079-3197/3/2/177/pdf?version=1429086192","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006686201","display_name":"Raymond J. Moran","orcid":null},"institutions":[{"id":"https://openalex.org/I42934936","display_name":"Dublin City University","ror":"https://ror.org/04a1a1e81","country_code":"IE","type":"education","lineage":["https://openalex.org/I42934936"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Raymond Moran","raw_affiliation_strings":["Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin,  Dublin 9, Ireland","Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Glasnevin, Dublin 9, Ireland","Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin, Dublin 9, Ireland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin,  Dublin 9, Ireland","institution_ids":["https://openalex.org/I42934936"]},{"raw_affiliation_string":"Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Glasnevin, Dublin 9, Ireland","institution_ids":["https://openalex.org/I42934936"]},{"raw_affiliation_string":"Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin, Dublin 9, Ireland","institution_ids":["https://openalex.org/I42934936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013255443","display_name":"Claire C. Morgan","orcid":"https://orcid.org/0000-0002-8191-3738"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Claire Morgan","raw_affiliation_strings":["National Heart and Lung Institute, Faculty of Medicine, Imperial College, London W12 0NN, UK"],"affiliations":[{"raw_affiliation_string":"National Heart and Lung Institute, Faculty of Medicine, Imperial College, London W12 0NN, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062328111","display_name":"Mary J. O\u2019Connell","orcid":"https://orcid.org/0000-0002-1877-1001"},"institutions":[{"id":"https://openalex.org/I42934936","display_name":"Dublin City University","ror":"https://ror.org/04a1a1e81","country_code":"IE","type":"education","lineage":["https://openalex.org/I42934936"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Mary O'Connell","raw_affiliation_strings":["Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin,  Dublin 9, Ireland","Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Glasnevin, Dublin 9, Ireland","Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin, Dublin 9, Ireland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin,  Dublin 9, Ireland","institution_ids":["https://openalex.org/I42934936"]},{"raw_affiliation_string":"Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Glasnevin, Dublin 9, Ireland","institution_ids":["https://openalex.org/I42934936"]},{"raw_affiliation_string":"Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin, Dublin 9, Ireland","institution_ids":["https://openalex.org/I42934936"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062328111"],"corresponding_institution_ids":["https://openalex.org/I42934936"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":4.3612,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.93064919,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"3","issue":"2","first_page":"177","last_page":"196"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9993000030517578,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9970999956130981,"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":0.9922999739646912,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8324257731437683},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.633151113986969},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5887852311134338},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5802795886993408},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46983999013900757},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.44489920139312744},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.43281078338623047},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42958033084869385},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.41664204001426697},{"id":"https://openalex.org/keywords/mammal","display_name":"Mammal","score":0.41258540749549866},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.399684876203537},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3810526728630066},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3677903413772583},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31509822607040405},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.2382104992866516},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18669569492340088},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0920872688293457},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07887232303619385}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8324257731437683},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.633151113986969},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5887852311134338},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5802795886993408},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46983999013900757},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.44489920139312744},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43281078338623047},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42958033084869385},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.41664204001426697},{"id":"https://openalex.org/C2778234026","wikidata":"https://www.wikidata.org/wiki/Q7377","display_name":"Mammal","level":2,"score":0.41258540749549866},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.399684876203537},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3810526728630066},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3677903413772583},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31509822607040405},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.2382104992866516},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18669569492340088},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0920872688293457},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07887232303619385},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/computation3020177","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3020177","pdf_url":"https://www.mdpi.com/2079-3197/3/2/177/pdf?version=1429086192","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:c91caeb0619a437aaf85a0c8429e7b76","is_oa":true,"landing_page_url":"https://doaj.org/article/c91caeb0619a437aaf85a0c8429e7b76","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 2, Pp 177-196 (2015)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2079-3197/3/2/177/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/computation3020177","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/computation3020177","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3020177","pdf_url":"https://www.mdpi.com/2079-3197/3/2/177/pdf?version=1429086192","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321056","display_name":"Irish Research Council","ror":"https://ror.org/051xex213"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1976923174.pdf","grobid_xml":"https://content.openalex.org/works/W1976923174.grobid-xml"},"referenced_works_count":92,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W420957490","https://openalex.org/W1525734744","https://openalex.org/W1593676244","https://openalex.org/W1638753340","https://openalex.org/W1703729266","https://openalex.org/W1936769609","https://openalex.org/W1966972227","https://openalex.org/W1975933692","https://openalex.org/W1987624822","https://openalex.org/W1989229462","https://openalex.org/W1993798543","https://openalex.org/W1996019265","https://openalex.org/W1996912487","https://openalex.org/W2003447082","https://openalex.org/W2010026647","https://openalex.org/W2013298312","https://openalex.org/W2016811301","https://openalex.org/W2020693578","https://openalex.org/W2026881360","https://openalex.org/W2029226703","https://openalex.org/W2031700956","https://openalex.org/W2032666646","https://openalex.org/W2036684328","https://openalex.org/W2044732887","https://openalex.org/W2045160404","https://openalex.org/W2045656233","https://openalex.org/W2051254500","https://openalex.org/W2052337946","https://openalex.org/W2056760934","https://openalex.org/W2057619847","https://openalex.org/W2059359550","https://openalex.org/W2062018285","https://openalex.org/W2062355909","https://openalex.org/W2062447320","https://openalex.org/W2071467238","https://openalex.org/W2082928585","https://openalex.org/W2087520649","https://openalex.org/W2096702350","https://openalex.org/W2100945839","https://openalex.org/W2101768075","https://openalex.org/W2102424972","https://openalex.org/W2102507175","https://openalex.org/W2102736136","https://openalex.org/W2104398544","https://openalex.org/W2105006906","https://openalex.org/W2107808362","https://openalex.org/W2108187446","https://openalex.org/W2114035821","https://openalex.org/W2115031948","https://openalex.org/W2115888213","https://openalex.org/W2116709453","https://openalex.org/W2117337499","https://openalex.org/W2117443107","https://openalex.org/W2122057759","https://openalex.org/W2124161652","https://openalex.org/W2124511083","https://openalex.org/W2126632900","https://openalex.org/W2128841626","https://openalex.org/W2129747243","https://openalex.org/W2133870991","https://openalex.org/W2138009108","https://openalex.org/W2138309709","https://openalex.org/W2141913814","https://openalex.org/W2143210482","https://openalex.org/W2144377499","https://openalex.org/W2144654387","https://openalex.org/W2144934389","https://openalex.org/W2147307434","https://openalex.org/W2147660889","https://openalex.org/W2152298208","https://openalex.org/W2153800802","https://openalex.org/W2154036437","https://openalex.org/W2155622507","https://openalex.org/W2155836971","https://openalex.org/W2156521045","https://openalex.org/W2159310387","https://openalex.org/W2163627198","https://openalex.org/W2168573791","https://openalex.org/W2168696662","https://openalex.org/W2316705841","https://openalex.org/W2797148637","https://openalex.org/W3142322755","https://openalex.org/W4206702770","https://openalex.org/W4211177544","https://openalex.org/W4230357098","https://openalex.org/W4248681815","https://openalex.org/W4301347335","https://openalex.org/W6631401015","https://openalex.org/W6640617744","https://openalex.org/W6647473913","https://openalex.org/W6678592595"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2375383082","https://openalex.org/W2362218761","https://openalex.org/W2604174992","https://openalex.org/W1974895455"],"abstract_inverted_index":{"There":[0],"are":[1],"numerous":[2],"phylogenetic":[3,18],"reconstruction":[4,47],"methods":[5],"and":[6,13,27,39,63,119,127],"models":[7,114,131],"available\u2014but":[8],"which":[9,48],"should":[10],"you":[11],"use":[12,82],"why?":[14],"Important":[15],"considerations":[16],"in":[17,33,78,115,125],"analyses":[19],"include":[20],"data":[21],"quality,":[22],"structure,":[23],"signal,":[24],"alignment":[25],"length":[26],"sampling.":[28],"If":[29],"poorly":[30],"modelled,":[31],"variation":[32],"rates":[34],"of":[35,55,61,85,88,91,103],"change":[36],"across":[37,40],"proteins":[38],"lineages":[41],"can":[42,49,68],"lead":[43,51],"to":[44,52,98],"incorrect":[45],"phylogeny":[46],"then":[50],"downstream":[53],"misinterpretation":[54],"the":[56,83,86,89,100,122],"underlying":[57],"data.":[58],"The":[59],"risk":[60],"choosing":[62],"applying":[64],"an":[65],"inappropriate":[66],"model":[67,104],"be":[69],"reduced":[70],"with":[71],"some":[72],"critical":[73],"yet":[74],"straightforward":[75],"steps":[76,123],"outlined":[77],"this":[79,107],"paper.":[80],"We":[81],"question":[84],"position":[87],"root":[90],"placental":[92],"mammals":[93],"as":[94],"our":[95],"working":[96],"example":[97],"illustrate":[99],"topological":[101],"impact":[102],"misspecification.":[105],"Using":[106],"case":[108],"study":[109],"we":[110,120],"focus":[111],"on":[112],"using":[113],"a":[116],"Bayesian":[117],"framework":[118],"outline":[121],"involved":[124],"identifying":[126],"assessing":[128],"better":[129],"fitting":[130],"for":[132],"specific":[133],"datasets.":[134]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}