{"id":"https://openalex.org/W2102840198","doi":"https://doi.org/10.1093/bioinformatics/btq205","title":"Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data","display_name":"Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data","publication_year":2010,"publication_date":"2010-06-01","ids":{"openalex":"https://openalex.org/W2102840198","doi":"https://doi.org/10.1093/bioinformatics/btq205","mag":"2102840198","pmid":"https://pubmed.ncbi.nlm.nih.gov/20529898"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq205","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/12/i132/48856713/bioinformatics_26_12_i132.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/26/12/i132/48856713/bioinformatics_26_12_i132.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025640090","display_name":"Alexandros Stamatakis","orcid":"https://orcid.org/0000-0003-0353-0691"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alexandros Stamatakis","raw_affiliation_strings":["The Exelixis Lab (I12), Department of Computer Science, Technische Universit\u00e4t M\u00fcnchen, Boltzmannstr. 3, D-85748, Garching b. M\u00fcnchen, Germany"],"affiliations":[{"raw_affiliation_string":"The Exelixis Lab (I12), Department of Computer Science, Technische Universit\u00e4t M\u00fcnchen, Boltzmannstr. 3, D-85748, Garching b. M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010135755","display_name":"Nikolaos Alachiotis","orcid":"https://orcid.org/0000-0001-8162-3792"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nikolaos Alachiotis","raw_affiliation_strings":["The Exelixis Lab (I12), Department of Computer Science, Technische Universit\u00e4t M\u00fcnchen, Boltzmannstr. 3, D-85748, Garching b. M\u00fcnchen, Germany"],"affiliations":[{"raw_affiliation_string":"The Exelixis Lab (I12), Department of Computer Science, Technische Universit\u00e4t M\u00fcnchen, Boltzmannstr. 3, D-85748, Garching b. M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025640090"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.0331,"has_fulltext":false,"cited_by_count":129,"citation_normalized_percentile":{"value":0.86384173,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"26","issue":"12","first_page":"i132","last_page":"i139"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9894000291824341,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9704999923706055,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6614634394645691},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.5567392110824585},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5466528534889221},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.4219942092895508},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3948800563812256},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3686258792877197},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20460361242294312},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.19121438264846802},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1902599036693573},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1835072934627533}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6614634394645691},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.5567392110824585},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5466528534889221},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.4219942092895508},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3948800563812256},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3686258792877197},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20460361242294312},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.19121438264846802},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1902599036693573},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1835072934627533},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq205","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/12/i132/48856713/bioinformatics_26_12_i132.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:20529898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20529898","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:pubmedcentral.nih.gov:2881390","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2881390","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq205","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/12/i132/48856713/bioinformatics_26_12_i132.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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2102840198.pdf","grobid_xml":"https://content.openalex.org/works/W2102840198.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W611834007","https://openalex.org/W1549396587","https://openalex.org/W1562420726","https://openalex.org/W1593676244","https://openalex.org/W2011114339","https://openalex.org/W2031611770","https://openalex.org/W2062018285","https://openalex.org/W2099714380","https://openalex.org/W2102424972","https://openalex.org/W2103088017","https://openalex.org/W2103546861","https://openalex.org/W2124790653","https://openalex.org/W2136485386","https://openalex.org/W2146058063","https://openalex.org/W2150097277","https://openalex.org/W2158847865","https://openalex.org/W2159310387","https://openalex.org/W2168696662","https://openalex.org/W3142322755","https://openalex.org/W6632799381","https://openalex.org/W6675475285"],"related_works":["https://openalex.org/W4380150146","https://openalex.org/W3024870410","https://openalex.org/W2410652950","https://openalex.org/W4283773154","https://openalex.org/W3139174110","https://openalex.org/W4289597203","https://openalex.org/W2085630472","https://openalex.org/W1977098485","https://openalex.org/W4285201053","https://openalex.org/W4256612600"],"abstract_inverted_index":{"Current":[0],"open-source":[1],"version":[2],"of":[3],"RAxML":[4],"v7.2.6":[5],"available":[6],"at":[7],"http://wwwkramer.in.tum.de/exelixis/software.html.":[8]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
