{"id":"https://openalex.org/W128985141","doi":"https://doi.org/10.1007/978-1-62703-646-7_10","title":"Phylogeny-aware alignment with PRANK","display_name":"Phylogeny-aware alignment with PRANK","publication_year":2013,"publication_date":"2013-08-23","ids":{"openalex":"https://openalex.org/W128985141","doi":"https://doi.org/10.1007/978-1-62703-646-7_10","mag":"128985141","pmid":"https://pubmed.ncbi.nlm.nih.gov/24170401"},"language":"en","primary_location":{"id":"doi:10.1007/978-1-62703-646-7_10","doi":"https://doi.org/10.1007/978-1-62703-646-7_10","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-62703-646-7_10","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},"parent_works":[{"id":"https://openalex.org/W2407405674","display_name":"Multiple Sequence Alignment Methods","relationship":"volume"}],"lineage":["https://openalex.org/W128985141","https://openalex.org/W2407405674"],"child_works_count":0,"type":"book-chapter","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000878403","display_name":"Ari L\u00f6ytynoja","orcid":"https://orcid.org/0000-0001-5389-6611","observed_orcids":["https://orcid.org/0000-0001-5389-6611"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Ari L\u00f6ytynoja","raw_affiliation_strings":["Institute of Biotechnology, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000878403"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":null,"apc_paid":null,"fwci":14.1519,"has_fulltext":false,"cited_by_count":785,"citation_normalized_percentile":{"value":0.99336028,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"1079","issue":null,"first_page":"155","last_page":"170"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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":0.9990000128746033,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.00019999999494757503,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":9.999999747378752e-05,"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/pranks","display_name":"pranks","score":0.8320000171661377},{"id":"https://openalex.org/keywords/evolutionary-homology","display_name":"evolutionary homology","score":0.7009999752044678},{"id":"https://openalex.org/keywords/structural-homology","display_name":"structural homology","score":0.8650000095367432},{"id":"https://openalex.org/keywords/ancestral-sequence-reconstruction","display_name":"ancestral sequence reconstruction","score":0.8840000033378601},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.40400001406669617}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.649357795715332},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4787246882915497},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.47832465171813965},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4199545681476593},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3324536979198456},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11794096231460571},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0968177318572998}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":true},{"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":true}],"locations_count":2,"locations":[{"id":"doi:10.1007/978-1-62703-646-7_10","doi":"https://doi.org/10.1007/978-1-62703-646-7_10","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-62703-646-7_10","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},{"id":"pmid:24170401","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24170401","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,"listed_in":[],"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":"Methods in molecular biology (Clifton, N.J.)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1646393397","https://openalex.org/W1969153299","https://openalex.org/W1984814148","https://openalex.org/W1996681309","https://openalex.org/W2007668764","https://openalex.org/W2017777683","https://openalex.org/W2065973977","https://openalex.org/W2067150932","https://openalex.org/W2090748603","https://openalex.org/W2107511706","https://openalex.org/W2132926880","https://openalex.org/W2133437368","https://openalex.org/W2137015675","https://openalex.org/W2154099008","https://openalex.org/W2155320525","https://openalex.org/W2159235552","https://openalex.org/W2167133711"],"related_works":["https://openalex.org/W3111451490","https://openalex.org/W2524750053","https://openalex.org/W1984814148","https://openalex.org/W2017777683","https://openalex.org/W2588315559","https://openalex.org/W2183485040","https://openalex.org/W2101072339","https://openalex.org/W2066615914","https://openalex.org/W3185594128","https://openalex.org/W2128201162"],"abstract_inverted_index":{"Evolutionary":[0,10],"analyses":[1],"require":[2],"sequence":[3,19],"alignments":[4,20,52],"that":[5],"correctly":[6],"represent":[7],"evolutionary":[8,54,128,171],"homology.":[9],"and":[11,18,34,93,108,143,152,162,178],"structural":[12,26],"homology":[13],"are":[14,158],"not":[15],"the":[16,43,78,88,98,106,110,124,127,131,140,146,150,166,187],"same":[17],"generated":[21],"with":[22],"methods":[23,180],"designed":[24],"for":[25,53,165],"matching":[27],"can":[28,96,134,183],"be":[29,135,184],"seriously":[30],"misleading":[31],"in":[32,42,118,139,160,170],"comparative":[33],"phylogenetic":[35,64],"analyses.":[36],"The":[37,175],"phylogeny-aware":[38],"alignment":[39,58,68,111],"algorithm":[40,125],"implemented":[41],"program":[44,188],"PRANK":[45,60,95,133,169,176],"has":[46],"been":[47],"shown":[48],"to":[49,66,137],"produce":[50],"good":[51],"inferences.":[55],"Unlike":[56],"other":[57,179],"programs,":[59],"makes":[61],"use":[62,167],"of":[63,81,87,91,105,130,154,168],"information":[65],"distinguish":[67],"gaps":[69,112],"caused":[70],"by":[71],"insertions":[72,92],"or":[73,120],"deletions":[74],"and,":[75],"thereafter,":[76],"handles":[77],"two":[79],"types":[80],"events":[82],"differently.":[83],"As":[84,123],"a":[85,103],"by-product":[86],"correct":[89],"handling":[90],"deletions,":[94],"provide":[97],"inferred":[99],"ancestral":[100],"sequences":[101],"as":[102],"part":[104],"output":[107],"mark":[109],"differently":[113],"depending":[114],"on":[115,145],"their":[116],"origin":[117,151],"insertion":[119],"deletion":[121],"events.":[122],"infers":[126],"history":[129],"sequences,":[132],"sensitive":[136],"errors":[138],"guide":[141],"phylogeny":[142],"violations":[144],"underlying":[147],"assumptions":[148],"about":[149],"patterns":[153],"gaps.":[155],"These":[156],"issues":[157],"discussed":[159,181],"detail":[161],"practical":[163],"advice":[164],"analysis":[172],"is":[173],"provided.":[174],"software":[177],"here":[182],"found":[185],"from":[186],"home":[189],"page":[190],"at":[191],"http://code.google.com/p/prank-msa/.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":85},{"year":2025,"cited_by_count":92},{"year":2024,"cited_by_count":69},{"year":2023,"cited_by_count":84},{"year":2022,"cited_by_count":98},{"year":2021,"cited_by_count":112},{"year":2020,"cited_by_count":95},{"year":2019,"cited_by_count":56},{"year":2018,"cited_by_count":31},{"year":2017,"cited_by_count":28},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":3}],"updated_date":"2026-11-15T12:55:33.944570","created_date":"2016-06-24T00:00:00"}