{"id":"https://openalex.org/W1548223554","doi":"https://doi.org/10.1186/s12859-015-0619-8","title":"Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off","display_name":"Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off","publication_year":2015,"publication_date":"2015-06-08","ids":{"openalex":"https://openalex.org/W1548223554","doi":"https://doi.org/10.1186/s12859-015-0619-8","mag":"1548223554","pmid":"https://pubmed.ncbi.nlm.nih.gov/26055961"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0619-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0619-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0619-8","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/s12859-015-0619-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068172126","display_name":"Julien Y. Dutheil","orcid":"https://orcid.org/0000-0001-7753-4121"},"institutions":[{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210152351","display_name":"Max Planck Institute for Evolutionary Biology","ror":"https://ror.org/0534re684","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210152351"]}],"countries":["DE","FR"],"is_corresponding":true,"raw_author_name":"Julien Y Dutheil","raw_affiliation_strings":["Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Pl\u00f6n, 24306, Germany. dutheil@evolbio.mpg.de","Institut des Sciences de l'\u00c9volution - Montpellier, Place Eug\u00e8ne Bataillon - C.C. 065 -, Montpellier, 34095, France. dutheil@evolbio.mpg.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Pl\u00f6n, 24306, Germany. dutheil@evolbio.mpg.de","institution_ids":["https://openalex.org/I4210152351"]},{"raw_affiliation_string":"Institut des Sciences de l'\u00c9volution - Montpellier, Place Eug\u00e8ne Bataillon - C.C. 065 -, Montpellier, 34095, France. dutheil@evolbio.mpg.de","institution_ids":["https://openalex.org/I4210105943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012749986","display_name":"Emeric Figuet","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emeric Figuet","raw_affiliation_strings":["Institut des Sciences de l'\u00c9volution - Montpellier, Place Eug\u00e8ne Bataillon - C.C. 065 -, Montpellier, 34095, France. emeric.figuet@univ-montp2.fr"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut des Sciences de l'\u00c9volution - Montpellier, Place Eug\u00e8ne Bataillon - C.C. 065 -, Montpellier, 34095, France. emeric.figuet@univ-montp2.fr","institution_ids":["https://openalex.org/I4210105943"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5068172126"],"corresponding_institution_ids":["https://openalex.org/I4210105943","https://openalex.org/I4210152351"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":1543,"currency":"EUR","value_usd":1664},"fwci":0.2754,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.57716948,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"16","issue":"1","first_page":"190","last_page":"190"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.982699990272522,"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":0.982699990272522,"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":0.004000000189989805,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.001500000013038516,"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/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.8104985952377319},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.7198944687843323},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5998106598854065},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.594680666923523},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.480244904756546},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4723067283630371},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.46301907300949097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45765388011932373},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42604804039001465},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4147224426269531},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3749867081642151},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3655809760093689},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34236258268356323},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26681822538375854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2590569853782654},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15439340472221375},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.11321982741355896}],"concepts":[{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.8104985952377319},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.7198944687843323},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5998106598854065},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.594680666923523},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.480244904756546},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4723067283630371},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.46301907300949097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45765388011932373},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42604804039001465},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4147224426269531},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3749867081642151},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3655809760093689},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34236258268356323},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26681822538375854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2590569853782654},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15439340472221375},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.11321982741355896},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0619-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0619-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0619-8","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:26055961","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26055961","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:pubmedcentral.nih.gov:4459672","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4459672","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.mpg.de:item_2167944","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0027-AD52-0","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0619-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0619-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0619-8","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":[{"display_name":"Life in Land","score":0.5899999737739563,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1548223554.pdf","grobid_xml":"https://content.openalex.org/works/W1548223554.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1963957860","https://openalex.org/W1969901779","https://openalex.org/W2031611770","https://openalex.org/W2048154580","https://openalex.org/W2057108285","https://openalex.org/W2097606916","https://openalex.org/W2097730814","https://openalex.org/W2101443157","https://openalex.org/W2107794977","https://openalex.org/W2107867854","https://openalex.org/W2108795433","https://openalex.org/W2115888213","https://openalex.org/W2116087481","https://openalex.org/W2121052765","https://openalex.org/W2130909239","https://openalex.org/W2133437368","https://openalex.org/W2140771555","https://openalex.org/W2147526198","https://openalex.org/W2151409320","https://openalex.org/W2155469822","https://openalex.org/W2163255492","https://openalex.org/W2163352757","https://openalex.org/W2168491980","https://openalex.org/W2410633819","https://openalex.org/W6691548924"],"related_works":["https://openalex.org/W88386512","https://openalex.org/W4200088497","https://openalex.org/W1725737257","https://openalex.org/W2184990081","https://openalex.org/W3000366369","https://openalex.org/W2051319991","https://openalex.org/W2369516681","https://openalex.org/W3119443523","https://openalex.org/W2317368819","https://openalex.org/W2350198651"],"abstract_inverted_index":{"BACKGROUND:":[0],"Comparative":[1],"analysis":[2,30,268],"of":[3,9,42,52,57,66,80,88,98,108,121,141,148,152,167,174,180,194,197,226,229,243,277],"homologous":[4],"sequences":[5,67,109,149,238],"enables":[6],"the":[7,13,17,22,50,53,64,77,106,115,119,130,139,146,168,171,213,224,227,241],"understanding":[8],"evolutionary":[10],"patterns":[11],"at":[12,287],"molecular":[14],"level,":[15],"unraveling":[16],"functional":[18],"constraints":[19],"that":[20,202,252],"shaped":[21],"underlying":[23],"genes.":[24],"Bioinformatic":[25],"pipelines":[26],"for":[27,34,69,138,164,212],"comparative":[28,267],"sequence":[29,43,61,142,175,181,234],"typically":[31,73],"include":[32],"procedures":[33],"(i)":[35],"alignment":[36,82,235,272],"quality":[37,273],"assessment":[38,274],"and":[39,55,92,118,182,275],"(ii)":[40],"control":[41,51,225,276],"redundancy.":[44],"An":[45,280],"additional,":[46],"underassessed":[47],"step":[48,261],"is":[49,285],"amount":[54],"distribution":[56,228],"missing":[58,230,254],"data":[59,192,231,255],"in":[60,90,129,220,232,258,266],"alignments.":[62],"While":[63],"number":[65,147,151,242],"available":[68,286],"a":[70,112,158,246],"given":[71,103],"gene":[72,198],"increases":[74,206],"with":[75,123,177,245,271],"time,":[76],"site-specific":[78,204],"coverage":[79,125,205],"each":[81,165],"position":[83],"remains":[84],"highly":[85],"variable":[86],"because":[87,97],"differences":[89],"sequencing":[91],"annotation":[93],"quality,":[94],"or":[95],"simply":[96],"biological":[99],"variation.":[100],"For":[101],"any":[102,233],"alignment-based":[104],"analysis,":[105],"selection":[107,173],"thus":[110],"defines":[111],"trade-off":[113],"between":[114],"species":[116,214],"representation":[117],"quantity":[120],"sites":[122,153,244],"sufficient":[124],"to":[126,145,161,189,239],"be":[127,208,264],"included":[128],"subsequent":[131],"analyses.":[132],"RESULTS:":[133],"We":[134,250],"introduce":[135],"an":[136,259],"algorithm":[137,156,218],"optimization":[140,256],"alignments":[143],"according":[144],"vs.":[150],"trade-off.":[154],"The":[155,217],"uses":[157],"guide":[159],"tree":[160],"compute":[162],"scores":[163],"bipartition":[166],"alignment,":[169],"allowing":[170],"recursive":[172],"subsets":[176],"optimal":[178],"combinations":[179],"site":[183],"numbers.":[184],"By":[185],"applying":[186],"our":[187,253],"methods":[188],"two":[190],"large":[191],"sets":[193],"several":[195],"thousands":[196],"families,":[199],"we":[200],"show":[201],"significant":[203],"can":[207],"achieved":[209],"while":[210],"controlling":[211],"representation.":[215],"CONCLUSIONS:":[216],"introduced":[219],"this":[221],"work":[222],"allows":[223],"by":[236],"removing":[237],"increase":[240],"defined":[247],"minimum":[248],"coverage.":[249],"advocate":[251],"procedure":[257],"important":[260],"which":[262],"should":[263],"considered":[265],"pipelines,":[269],"together":[270],"sampled":[278],"diversity.":[279],"open":[281],"source":[282],"C++":[283],"implementation":[284],"http://bioweb.me/physamp.":[288]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
