{"id":"https://openalex.org/W2009525409","doi":"https://doi.org/10.1111/cla.12113","title":"Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP","display_name":"Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP","publication_year":2015,"publication_date":"2015-03-10","ids":{"openalex":"https://openalex.org/W2009525409","doi":"https://doi.org/10.1111/cla.12113","mag":"2009525409","pmid":"https://pubmed.ncbi.nlm.nih.gov/34732024"},"language":"en","primary_location":{"id":"doi:10.1111/cla.12113","doi":"https://doi.org/10.1111/cla.12113","is_oa":false,"landing_page_url":"https://doi.org/10.1111/cla.12113","pdf_url":null,"source":{"id":"https://openalex.org/S90511721","display_name":"Cladistics","issn_l":"0748-3007","issn":["0748-3007","1096-0031"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cladistics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109380622","display_name":"Barry G. Hall","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Barry G. Hall","raw_affiliation_strings":["Bellingham Research Institute Bellingham WA 98229 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bellingham Research Institute Bellingham WA 98229 USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5109380622"],"corresponding_institution_ids":[],"apc_list":{"value":3960,"currency":"USD","value_usd":3960},"apc_paid":null,"fwci":0.4235,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.53809684,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":87,"max":96},"biblio":{"volume":"32","issue":"1","first_page":"90","last_page":"99"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":0.0,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/single-nucleotide-polymorphisms","display_name":"single nucleotide polymorphisms","score":0.7210000157356262},{"id":"https://openalex.org/keywords/recombination","display_name":"recombination","score":0.6990000009536743},{"id":"https://openalex.org/keywords/sequence-diversity","display_name":"sequence diversity","score":0.972000002861023},{"id":"https://openalex.org/keywords/microbial-genomes","display_name":"microbial genomes","score":0.6639999747276306},{"id":"https://openalex.org/keywords/topological-accuracy","display_name":"topological accuracy","score":0.7950000166893005},{"id":"https://openalex.org/keywords/parsimony","display_name":"parsimony","score":0.6110000014305115},{"id":"https://openalex.org/keywords/maximum-likelihood-estimation","display_name":"maximum likelihood estimation","score":0.8899999856948853},{"id":"https://openalex.org/keywords/neighbor-joining","display_name":"neighbor-joining","score":0.9649999737739563}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7597737312316895},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.663830041885376},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.544640064239502},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5435012578964233},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5263389945030212},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.46650001406669617},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.46082034707069397},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.45657920837402344},{"id":"https://openalex.org/C98722961","wikidata":"https://www.wikidata.org/wiki/Q7189436","display_name":"Phylogenetic diversity","level":4,"score":0.45443055033683777},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4124400317668915},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3806276321411133},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26966243982315063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2422427535057068},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.15141579508781433}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1111/cla.12113","doi":"https://doi.org/10.1111/cla.12113","is_oa":false,"landing_page_url":"https://doi.org/10.1111/cla.12113","pdf_url":null,"source":{"id":"https://openalex.org/S90511721","display_name":"Cladistics","issn_l":"0748-3007","issn":["0748-3007","1096-0031"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cladistics","raw_type":"journal-article"},{"id":"pmid:34732024","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34732024","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,"listed_in":[],"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":"Cladistics : the international journal of the Willi Hennig Society","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1974599898","https://openalex.org/W1981292743","https://openalex.org/W2003265935","https://openalex.org/W2024398948","https://openalex.org/W2031611770","https://openalex.org/W2041257508","https://openalex.org/W2053576319","https://openalex.org/W2055298722","https://openalex.org/W2059410416","https://openalex.org/W2083539954","https://openalex.org/W2118442768","https://openalex.org/W2132632499","https://openalex.org/W2141052558","https://openalex.org/W2141735861","https://openalex.org/W2142402047","https://openalex.org/W2143007385","https://openalex.org/W2150550043","https://openalex.org/W2151371624","https://openalex.org/W2153700219","https://openalex.org/W2157991545","https://openalex.org/W2162195084","https://openalex.org/W2166666507","https://openalex.org/W3199943451"],"related_works":["https://openalex.org/W4388556896","https://openalex.org/W4220927687","https://openalex.org/W7098423497","https://openalex.org/W7095716098","https://openalex.org/W2168923292","https://openalex.org/W2177087965","https://openalex.org/W2155998147","https://openalex.org/W7098101089","https://openalex.org/W7101159939","https://openalex.org/W2730645161"],"abstract_inverted_index":{"kSNP":[0,25,61,78,188],"v2":[1],"is":[2,96,121,130,178,186,189],"a":[3,135,149],"powerful":[4],"tool":[5,192],"for":[6,17,193],"single":[7],"nucleotide":[8],"polymorphism":[9],"(SNP)":[10],"identification":[11],"from":[12,21,197],"complete":[13],"microbial":[14,198],"genomes":[15],"and":[16,39,63,70,163,165,171,205],"estimating":[18,194],"phylogenetic":[19,195],"trees":[20,62,79,108,196],"the":[22,57,66,124,131,138,166,172],"identified":[23],"SNPs.":[24],"can":[26],"analyse":[27],"finished":[28],"genomes,":[29],"genome":[30,44,199],"assemblies,":[31],"raw":[32],"reads":[33],"or":[34,46],"any":[35],"combination":[36],"of":[37,60,68,77,127,133,137,140,146,151,174,183],"those":[38,113],"does":[40],"not":[41],"require":[42],"either":[43],"alignment":[45],"reference":[47],"genomes.":[48],"This":[49],"study":[50,185],"uses":[51],"sequence":[52,206],"evolution":[53],"simulations":[54],"to":[55,64,142,156,159,176],"evaluate":[56],"topological":[58,118,128,169],"accuracy":[59,88,91,105,129,170],"assess":[65],"effects":[67],"diversity":[69,207],"recombination":[71,103,204],"on":[72],"that":[73,114,123,187,202],"accuracy.":[74,94,119],"The":[75,180],"accuracies":[76],"are":[80,109,154,208],"strongly":[81,98],"affected":[82],"by":[83,100],"increasing":[84],"diversity,":[85],"with":[86],"parsimony":[87],">":[89,92],"maximum-likelihood":[90],"neighbour-joining":[93],"Accuracy":[95],"also":[97],"influenced":[99],"recombination;":[101],"as":[102,112],"increases":[104],"decreases.":[106],"Reliable":[107],"arbitrarily":[110],"defined":[111],"have":[115],"\u2265":[116],"90%":[117],"It":[120],"determined":[122],"best":[125],"predictor":[126],"ratio":[132,173],"r/m,":[134],"measure":[136,150],"effect":[139],"recombination,":[141],"FCK":[143,177],"(the":[144],"fraction":[145],"core":[147],"kmers),":[148],"diversity.":[152],"Tools":[153],"available":[155],"allow":[157],"investigators":[158],"determine":[160],"both":[161,203],"r/m":[162,175],"FCK,":[164],"relationship":[167],"between":[168],"determined.":[179],"practical":[181],"implication":[182],"this":[184],"an":[190],"effective":[191],"sequences":[200],"provided":[201],"within":[209],"acceptable":[210],"ranges.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2016-06-24T00:00:00"}
