{"id":"https://openalex.org/W2161722223","doi":"https://doi.org/10.1093/bioinformatics/btv541","title":"markophylo: Markov chain analysis on phylogenetic trees","display_name":"markophylo: Markov chain analysis on phylogenetic trees","publication_year":2015,"publication_date":"2015-09-11","ids":{"openalex":"https://openalex.org/W2161722223","doi":"https://doi.org/10.1093/bioinformatics/btv541","mag":"2161722223","pmid":"https://pubmed.ncbi.nlm.nih.gov/26363176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv541","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv541","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/130/16920036/btv541.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/130/16920036/btv541.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037406350","display_name":"Utkarsh J. Dang","orcid":"https://orcid.org/0000-0003-4120-2015"},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Utkarsh J. Dang","raw_affiliation_strings":["Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada","institution_ids":["https://openalex.org/I98251732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045219735","display_name":"G. Brian Golding","orcid":"https://orcid.org/0000-0002-7575-0282"},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"G. Brian Golding","raw_affiliation_strings":["Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada","institution_ids":["https://openalex.org/I98251732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5037406350"],"corresponding_institution_ids":["https://openalex.org/I98251732"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8268,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.72480592,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"32","issue":"1","first_page":"130","last_page":"132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8798999786376953,"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":0.8798999786376953,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.060100000351667404,"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/T10012","display_name":"Genetic diversity and population structure","score":0.018300000578165054,"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/markov-chain","display_name":"Markov chain","score":0.7383826971054077},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7064647674560547},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6530895233154297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6241781115531921},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5292277336120605},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.5288345217704773},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.5255666971206665},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34728026390075684},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33880847692489624},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.32871943712234497},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.27425551414489746},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23986488580703735},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2335871458053589},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.19135484099388123},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.13873526453971863},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12561774253845215},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10397756099700928},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.101421058177948}],"concepts":[{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.7383826971054077},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7064647674560547},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6530895233154297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6241781115531921},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5292277336120605},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.5288345217704773},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.5255666971206665},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34728026390075684},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33880847692489624},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.32871943712234497},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.27425551414489746},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23986488580703735},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2335871458053589},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.19135484099388123},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.13873526453971863},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12561774253845215},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10397756099700928},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.101421058177948}],"mesh":[{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btv541","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv541","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/130/16920036/btv541.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26363176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26363176","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv541","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv541","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/1/130/16920036/btv541.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320315254","display_name":"Innovative Research Group Project of the National Natural Science Foundation of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161722223.pdf","grobid_xml":"https://content.openalex.org/works/W2161722223.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W585037855","https://openalex.org/W1525734744","https://openalex.org/W1990631742","https://openalex.org/W2006274528","https://openalex.org/W2058815839","https://openalex.org/W2096484952","https://openalex.org/W2103581172","https://openalex.org/W2104515939","https://openalex.org/W2106201557","https://openalex.org/W2107991904","https://openalex.org/W2122082385","https://openalex.org/W2124790653","https://openalex.org/W2126424265","https://openalex.org/W2139265147","https://openalex.org/W2143361590","https://openalex.org/W2148592495","https://openalex.org/W2151409320","https://openalex.org/W2159325249","https://openalex.org/W2168175751","https://openalex.org/W2171059556","https://openalex.org/W2582743722","https://openalex.org/W4248740947","https://openalex.org/W4250847479","https://openalex.org/W6652004016","https://openalex.org/W6665272994"],"related_works":["https://openalex.org/W2084326697","https://openalex.org/W2027903142","https://openalex.org/W2354322608","https://openalex.org/W2804608325","https://openalex.org/W2077211377","https://openalex.org/W2186675474","https://openalex.org/W2387462590","https://openalex.org/W2056274461","https://openalex.org/W2368739446","https://openalex.org/W2010321967"],"abstract_inverted_index":{"SUMMARY:":[0],"Continuous-time":[1],"Markov":[2,119],"chain":[3],"models":[4,41,56,117],"with":[5,42,128,162,168],"finite":[6],"state":[7],"space":[8],"are":[9,178],"routinely":[10],"used":[11,49],"for":[12,75,81],"analysis":[13],"of":[14,22,102],"discrete":[15,24,103],"character":[16,25],"data":[17,26,177],"on":[18,105,121],"phylogenetic":[19,122],"trees.":[20,123],"Examples":[21],"such":[23],"include":[27],"restriction":[28],"sites,":[29],"gene":[30,36],"family":[31,37],"presence/absence,":[32],"intron":[33],"presence/absence":[34],"and":[35,92,135],"size":[38],"data.":[39],"While":[40],"constrained":[43],"substitution":[44],"rate":[45,68],"matrices":[46],"have":[47,57],"been":[48,58],"to":[50,85],"good":[51],"effect,":[52],"more":[53],"biologically":[54],"realistic":[55],"increasingly":[59],"implemented":[60],"in":[61,133,138],"the":[62,129,136,153,169],"recent":[63],"literature":[64],"combining,":[65],"e.g.,":[66],"site":[67,70],"variation,":[69],"partitioning,":[71],"branch-specific":[72],"rates,":[73],"allowing":[74],"non-stationary":[76],"prior":[77],"root":[78],"probabilities,":[79],"correcting":[80],"sampling":[82],"bias,":[83],"etc.":[84],"name":[86],"a":[87,90,106,109,148],"few.":[88],"Here,":[89],"flexible":[91],"fast":[93],"R":[94,150,155,170],"package":[95,125,151],"is":[96,126,145,165],"introduced":[97],"that":[98],"infers":[99],"evolutionary":[100],"rates":[101],"characters":[104],"tree":[107],"within":[108],"probabilistic":[110],"framework.":[111],"The":[112,124],"package,":[113],"markophylo,":[114],"fits":[115],"maximum-likelihood":[116],"using":[118],"chains":[120],"efficient,":[127],"workhorse":[130],"functions":[131],"written":[132],"C++":[134],"interface":[137],"user-friendly":[139],"R.":[140],"AVAILABILITY":[141],"AND":[142],"IMPLEMENTATION:":[143],"markophylo":[144],"available":[146,179],"as":[147],"platform-independent":[149],"from":[152],"Comprehensive":[154],"Archive":[156],"Network":[157],"at":[158,180],"https://cran.r-project.org/web/packages/markophylo/.":[159],"A":[160],"vignette":[161],"numerous":[163],"examples":[164],"also":[166],"provided":[167],"package.":[171],"CONTACT:":[172],"udang@mcmaster.ca":[173],"SUPPLEMENTARY":[174],"INFORMATION:":[175],"Supplementary":[176],"Bioinformatics":[181],"online.":[182]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}