{"id":"https://openalex.org/W1807494956","doi":"https://doi.org/10.1186/1471-2105-6-138","title":"libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny","display_name":"libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny","publication_year":2005,"publication_date":"2005-06-06","ids":{"openalex":"https://openalex.org/W1807494956","doi":"https://doi.org/10.1186/1471-2105-6-138","mag":"1807494956","pmid":"https://pubmed.ncbi.nlm.nih.gov/15938750"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-138","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-138","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-138","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-138","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026512773","display_name":"Davin Butt","orcid":null},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Davin Butt","raw_affiliation_strings":["Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada. davin@cs.dal.ca","Faculty of Computer Science, Dalhousie University, Halifax, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada. davin@cs.dal.ca","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Faculty of Computer Science, Dalhousie University, Halifax, Canada","institution_ids":["https://openalex.org/I129902397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053095410","display_name":"Andrew J. Roger","orcid":"https://orcid.org/0000-0003-1370-9820"},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Andrew J Roger","raw_affiliation_strings":["Canadian Institute for Advanced Research (CIAR), Canada","Dept. of Biochemistry and Molecular Biology, Dalhousie University, Tupper Medical Building, Halifax, NS, B3H 1X5, Canada","Dept. of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canadian Institute for Advanced Research (CIAR), Canada","institution_ids":["https://openalex.org/I109736498"]},{"raw_affiliation_string":"Dept. of Biochemistry and Molecular Biology, Dalhousie University, Tupper Medical Building, Halifax, NS, B3H 1X5, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Dept. of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada","institution_ids":["https://openalex.org/I129902397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054585121","display_name":"Christian Blouin","orcid":"https://orcid.org/0000-0002-4434-4142"},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Christian Blouin","raw_affiliation_strings":["Canadian Institute for Advanced Research (CIAR), Canada","Dept. of Biochemistry and Molecular Biology, Dalhousie University, Tupper Medical Building, Halifax, NS, B3H 1X5, Canada","Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada","Faculty of Computer Science, Dalhousie University, Halifax, Canada","Dept. of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canadian Institute for Advanced Research (CIAR), Canada","institution_ids":["https://openalex.org/I109736498"]},{"raw_affiliation_string":"Dept. of Biochemistry and Molecular Biology, Dalhousie University, Tupper Medical Building, Halifax, NS, B3H 1X5, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Faculty of Computer Science, Dalhousie University, Halifax, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Dept. of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada","institution_ids":["https://openalex.org/I129902397"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054585121"],"corresponding_institution_ids":["https://openalex.org/I109736498","https://openalex.org/I129902397"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.8844,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.70524901,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"6","issue":"1","first_page":"138","last_page":"138"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.883899986743927,"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":0.883899986743927,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.06949999928474426,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.00570000009611249,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7839535474777222},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6449059247970581},{"id":"https://openalex.org/keywords/mega","display_name":"Mega-","score":0.5536469221115112},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5161994099617004},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5022945404052734},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4886048436164856},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.46707963943481445},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4669526517391205},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4544149339199066},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.445100337266922},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4192701280117035},{"id":"https://openalex.org/keywords/computational-phylogenetics","display_name":"Computational phylogenetics","score":0.41772258281707764},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.40800076723098755},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3836537003517151},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.3767933249473572},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36821824312210083},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24245989322662354},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1924019455909729},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14013460278511047},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09920570254325867},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.09780186414718628}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7839535474777222},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6449059247970581},{"id":"https://openalex.org/C2781078984","wikidata":"https://www.wikidata.org/wiki/Q107205","display_name":"Mega-","level":2,"score":0.5536469221115112},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5161994099617004},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5022945404052734},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4886048436164856},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.46707963943481445},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4669526517391205},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4544149339199066},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.445100337266922},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4192701280117035},{"id":"https://openalex.org/C41168302","wikidata":"https://www.wikidata.org/wiki/Q3772859","display_name":"Computational phylogenetics","level":5,"score":0.41772258281707764},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.40800076723098755},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3836537003517151},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.3767933249473572},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36821824312210083},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24245989322662354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1924019455909729},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14013460278511047},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09920570254325867},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.09780186414718628},{"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/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"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":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-6-138","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-138","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-138","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15938750","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15938750","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:e9f9cc37d19c472cb3bed718b26122fe","is_oa":false,"landing_page_url":"https://doaj.org/article/e9f9cc37d19c472cb3bed718b26122fe","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 6, Iss 1, p 138 (2005)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:290608","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1175080","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1175080","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1175080","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-6-138","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-138","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-138","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.44999998807907104,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320326645","display_name":"Genome Atlantic","ror":null},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1807494956.pdf","grobid_xml":"https://content.openalex.org/works/W1807494956.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W127414535","https://openalex.org/W1564625264","https://openalex.org/W2016000389","https://openalex.org/W2017519756","https://openalex.org/W2022368654","https://openalex.org/W2037667459","https://openalex.org/W2051161693","https://openalex.org/W2062018285","https://openalex.org/W2097706568","https://openalex.org/W2112956791","https://openalex.org/W2125359798","https://openalex.org/W2141497252","https://openalex.org/W2141733457","https://openalex.org/W2147660889","https://openalex.org/W2153657280","https://openalex.org/W2163123197","https://openalex.org/W2170645178","https://openalex.org/W2577202510","https://openalex.org/W2601913882","https://openalex.org/W2622656037","https://openalex.org/W2977721658","https://openalex.org/W3199943451","https://openalex.org/W4233815609"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2133116680","https://openalex.org/W2111937814","https://openalex.org/W2141411672","https://openalex.org/W2091678889","https://openalex.org/W1482324242","https://openalex.org/W187239587","https://openalex.org/W88386512","https://openalex.org/W2588883198","https://openalex.org/W3113335767"],"abstract_inverted_index":{"BACKGROUND:":[0],"An":[1],"increasing":[2],"number":[3],"of":[4,38,87,104,131],"bioinformatics":[5,32],"methods":[6],"are":[7],"considering":[8],"the":[9,19,102,129],"phylogenetic":[10,22,105],"relationships":[11],"between":[12],"biological":[13,60],"sequences.":[14],"Implementing":[15],"new":[16],"methodologies":[17,127],"using":[18],"maximum":[20,49],"likelihood":[21,50],"framework":[23],"can":[24,63],"be":[25,64],"a":[26,36,43,55,84,111,119],"time":[27],"consuming":[28],"task.":[29],"RESULTS:":[30],"The":[31],"library":[33],"libcov":[34,62,116],"is":[35,94,117],"collection":[37],"C++":[39],"classes":[40],"that":[41,100],"provides":[42],"high":[44],"and":[45,54,80],"low-level":[46],"interface":[47],"to":[48,66,96,124],"phylogenetics,":[51],"sequence":[52],"analysis":[53],"data":[56],"structure":[57],"for":[58,83],"structural":[59],"methods.":[61],"used":[65],"compute":[67],"likelihoods,":[68],"search":[69],"tree":[70,78],"topologies,":[71],"estimate":[72],"site":[73],"rates,":[74],"cluster":[75],"sequences,":[76],"manipulate":[77],"structures":[79],"compare":[81],"phylogenies":[82],"broad":[85],"selection":[86],"applications.":[88],"CONCLUSION:":[89],"Using":[90],"this":[91],"library,":[92],"it":[93],"possible":[95],"rapidly":[97],"prototype":[98],"applications":[99],"use":[101],"sophistication":[103],"likelihoods":[106],"without":[107],"getting":[108],"involved":[109],"in":[110,128],"major":[112],"software":[113],"engineering":[114],"project.":[115],"thus":[118],"potentially":[120],"valuable":[121],"building":[122],"block":[123],"develop":[125],"in-house":[126],"field":[130],"protein":[132],"phylogenetics.":[133]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}