{"id":"https://openalex.org/W2950175395","doi":"https://doi.org/10.1093/bioinformatics/bty295","title":"Inference of species phylogenies from bi-allelic markers using pseudo-likelihood","display_name":"Inference of species phylogenies from bi-allelic markers using pseudo-likelihood","publication_year":2018,"publication_date":"2018-04-15","ids":{"openalex":"https://openalex.org/W2950175395","doi":"https://doi.org/10.1093/bioinformatics/bty295","mag":"2950175395","pmid":"https://pubmed.ncbi.nlm.nih.gov/29950004"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty295","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty295","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i376/25098516/bty295.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i376/25098516/bty295.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003087064","display_name":"Jiafan Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jiafan Zhu","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080534085","display_name":"Luay Nakhleh","orcid":"https://orcid.org/0000-0003-3288-6769"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Luay Nakhleh","raw_affiliation_strings":["Department of BioSciences, Rice University, Houston, TX, USA","Department of Computer Science, Rice University, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of BioSciences, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003087064","https://openalex.org/A5080534085"],"corresponding_institution_ids":["https://openalex.org/I74775410"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":9.9637,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.97763269,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"13","first_page":"i376","last_page":"i385"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9983000159263611,"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":0.9968000054359436,"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/coalescent-theory","display_name":"Coalescent theory","score":0.7024941444396973},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6343731880187988},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6150460839271545},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.464011549949646},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45529699325561523},{"id":"https://openalex.org/keywords/approximate-bayesian-computation","display_name":"Approximate Bayesian computation","score":0.4504564106464386},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.42706814408302307},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4151208996772766},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30870187282562256},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20940226316452026},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1179688572883606}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.7024941444396973},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6343731880187988},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6150460839271545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.464011549949646},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45529699325561523},{"id":"https://openalex.org/C2779377595","wikidata":"https://www.wikidata.org/wiki/Q21045424","display_name":"Approximate Bayesian computation","level":3,"score":0.4504564106464386},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.42706814408302307},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4151208996772766},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30870187282562256},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20940226316452026},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1179688572883606}],"mesh":[{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000483","descriptor_name":"Alleles","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":"D008957","descriptor_name":"Models, Genetic","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":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty295","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty295","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i376/25098516/bty295.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29950004","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29950004","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},{"id":"pmh:oai:europepmc.org:4991093","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022577","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:scholarship.rice.edu:1911/103318","is_oa":true,"landing_page_url":"http://hdl.handle.net/1911/103318","pdf_url":null,"source":{"id":"https://openalex.org/S4306400220","display_name":"Rice University's digital scholarship archive (Rice University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74775410","host_organization_name":"Rice University","host_organization_lineage":["https://openalex.org/I74775410"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty295","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty295","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i376/25098516/bty295.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2038780265","display_name":"AF: Medium: Statistical Inference of Complex Evolutionary Histories","funder_award_id":"1514177","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2929060337","display_name":null,"funder_award_id":"1355998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3733356924","display_name":null,"funder_award_id":"CCF-1302179","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4062440706","display_name":"MRI: Acquisition of Big-Data Private-Cloud Research Cyberinfrastructure (BDPC)","funder_award_id":"1338099","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5151224254","display_name":"RTG: Cross-Training in Statistics and Computer Science","funder_award_id":"1547433","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5402090779","display_name":null,"funder_award_id":"F-130","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5895462963","display_name":null,"funder_award_id":"DBI-1355998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5944038379","display_name":null,"funder_award_id":"CNS-1338099","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6445140754","display_name":null,"funder_award_id":"CCF-1514177","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6967614109","display_name":"AF: Medium: Algorithmic Foundations for Phylogenetic Networks","funder_award_id":"1302179","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7776630215","display_name":null,"funder_award_id":"DMS-1547433","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310133","display_name":"Rice University","ror":"https://ror.org/008zs3103"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950175395.pdf","grobid_xml":"https://content.openalex.org/works/W2950175395.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W285206176","https://openalex.org/W1493899324","https://openalex.org/W1558762228","https://openalex.org/W1638410732","https://openalex.org/W1849663075","https://openalex.org/W1892960895","https://openalex.org/W1897064680","https://openalex.org/W1979100126","https://openalex.org/W2049226423","https://openalex.org/W2058198256","https://openalex.org/W2091458978","https://openalex.org/W2102424972","https://openalex.org/W2110105435","https://openalex.org/W2110263284","https://openalex.org/W2117665706","https://openalex.org/W2121166240","https://openalex.org/W2123305821","https://openalex.org/W2124539629","https://openalex.org/W2126918260","https://openalex.org/W2131400772","https://openalex.org/W2139050004","https://openalex.org/W2148723086","https://openalex.org/W2160602082","https://openalex.org/W2172696783","https://openalex.org/W2198071255","https://openalex.org/W2289722224","https://openalex.org/W2345610960","https://openalex.org/W2566526826","https://openalex.org/W2951570719","https://openalex.org/W2952113249","https://openalex.org/W2952540487","https://openalex.org/W2952712909","https://openalex.org/W2962725223","https://openalex.org/W4210633230","https://openalex.org/W4241651029","https://openalex.org/W4256288253","https://openalex.org/W4388316067","https://openalex.org/W6610394884","https://openalex.org/W6685415645"],"related_works":["https://openalex.org/W4254268221","https://openalex.org/W2038264393","https://openalex.org/W147282674","https://openalex.org/W2112400707","https://openalex.org/W2101991559","https://openalex.org/W4300585845","https://openalex.org/W2152997891","https://openalex.org/W2951248153","https://openalex.org/W2840568513","https://openalex.org/W4287661213"],"abstract_inverted_index":{"The":[0],"methods":[1],"have":[2],"been":[3],"implemented":[4],"in":[5],"PhyloNet":[6],"(http://bioinfocs.rice.edu/phylonet).":[7]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":9}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
