{"id":"https://openalex.org/W3210608097","doi":"https://doi.org/10.1186/s12859-021-04442-8","title":"ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process","display_name":"ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process","publication_year":2021,"publication_date":"2021-10-24","ids":{"openalex":"https://openalex.org/W3210608097","doi":"https://doi.org/10.1186/s12859-021-04442-8","mag":"3210608097","pmid":"https://pubmed.ncbi.nlm.nih.gov/34689750"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04442-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04442-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04442-8","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/track/pdf/10.1186/s12859-021-04442-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029417733","display_name":"Massimo Maiolo","orcid":"https://orcid.org/0000-0001-5858-4182"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I858936495","display_name":"ZHAW Zurich University of Applied Sciences","ror":"https://ror.org/05pmsvm27","country_code":"CH","type":"education","lineage":["https://openalex.org/I858936495"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Massimo Maiolo","raw_affiliation_strings":["Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","institution_ids":["https://openalex.org/I858936495"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101940982","display_name":"Lorenzo Gatti","orcid":"https://orcid.org/0000-0001-5417-2797"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I858936495","display_name":"ZHAW Zurich University of Applied Sciences","ror":"https://ror.org/05pmsvm27","country_code":"CH","type":"education","lineage":["https://openalex.org/I858936495"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lorenzo Gatti","raw_affiliation_strings":["Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","institution_ids":["https://openalex.org/I858936495"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075290852","display_name":"Diego Frei","orcid":null},"institutions":[{"id":"https://openalex.org/I15196421","display_name":"University of Applied Sciences and Arts of Southern Switzerland","ror":"https://ror.org/05ep8g269","country_code":"CH","type":"education","lineage":["https://openalex.org/I15196421"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Diego Frei","raw_affiliation_strings":["Institute of Information Systems and Networking, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928, Manno, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Systems and Networking, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928, Manno, Switzerland","institution_ids":["https://openalex.org/I15196421"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031382797","display_name":"Tiziano Leidi","orcid":"https://orcid.org/0000-0002-6335-7977"},"institutions":[{"id":"https://openalex.org/I15196421","display_name":"University of Applied Sciences and Arts of Southern Switzerland","ror":"https://ror.org/05ep8g269","country_code":"CH","type":"education","lineage":["https://openalex.org/I15196421"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Tiziano Leidi","raw_affiliation_strings":["Institute of Information Systems and Networking, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928, Manno, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Systems and Networking, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928, Manno, Switzerland","institution_ids":["https://openalex.org/I15196421"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085414073","display_name":"M. Gil","orcid":"https://orcid.org/0000-0002-8406-8218"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I858936495","display_name":"ZHAW Zurich University of Applied Sciences","ror":"https://ror.org/05pmsvm27","country_code":"CH","type":"education","lineage":["https://openalex.org/I858936495"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Manuel Gil","raw_affiliation_strings":["Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","institution_ids":["https://openalex.org/I858936495"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046692009","display_name":"Maria Anisimova","orcid":"https://orcid.org/0000-0001-8145-7966"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I200744771","display_name":"ZHAW Zurich University of Applied Sciences","ror":null,"country_code":"CH","type":null,"lineage":["https://openalex.org/I200744771"]},{"id":"https://openalex.org/I858936495","display_name":"ZHAW Zurich University of Applied Sciences","ror":"https://ror.org/05pmsvm27","country_code":"CH","type":"education","lineage":["https://openalex.org/I858936495"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Maria Anisimova","raw_affiliation_strings":["Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland. maria.anisimova@zhaw.ch","Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland. maria.anisimova@zhaw.ch","Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland. maria.anisimova@zhaw.ch","institution_ids":["https://openalex.org/I200744771"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland. maria.anisimova@zhaw.ch","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Schloss 1, Postfach, 8820, W\u00e4denswil, Switzerland","institution_ids":["https://openalex.org/I858936495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046692009"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I200744771","https://openalex.org/I858936495"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":825,"currency":"EUR","value_usd":889},"fwci":0.9772,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.74998116,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"22","issue":"1","first_page":"518","last_page":"518"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9571999907493591,"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":0.9571999907493591,"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":0.016599999740719795,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.9176473021507263},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6863957047462463},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6734926700592041},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.6133919358253479},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5454621315002441},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5263030529022217},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5258070826530457},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.47897791862487793},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.46448713541030884},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.437051385641098},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.42595335841178894},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3256832957267761},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30585139989852905},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2884579300880432},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23251211643218994},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.220767080783844},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12974649667739868},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09937030076980591},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08711856603622437}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.9176473021507263},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6863957047462463},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6734926700592041},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.6133919358253479},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5454621315002441},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5263030529022217},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5258070826530457},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.47897791862487793},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.46448713541030884},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.437051385641098},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.42595335841178894},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3256832957267761},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30585139989852905},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2884579300880432},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23251211643218994},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.220767080783844},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12974649667739868},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09937030076980591},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08711856603622437},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"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":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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-021-04442-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04442-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04442-8","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:34689750","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34689750","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:digitalcollection.zhaw.ch:11475/23747","is_oa":true,"landing_page_url":"https://hdl.handle.net/11475/23747","pdf_url":null,"source":{"id":"https://openalex.org/S4306401811","display_name":"Z\u00fcrcher Hochschule f\u00fcr Angewandte Wissenschaften digital collection (Zurich University of Applied Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200744771","host_organization_name":"ZHAW Zurich University of Applied Sciences","host_organization_lineage":["https://openalex.org/I200744771"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:7dfe5f930a4641c0a758abf0e9bbde85","is_oa":true,"landing_page_url":"https://doaj.org/article/7dfe5f930a4641c0a758abf0e9bbde85","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-12 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7433075","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8543915","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8543915","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8543915","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04442-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04442-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04442-8","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":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G4975463037","display_name":"Fast joint estimation of alignment and phylogeny from genomic sequences in a frequentist framework","funder_award_id":"157064","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G6904009744","display_name":null,"funder_award_id":"31003A_176316","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7258255854","display_name":"Frequentist estimation of the evolutionary history of sequences with substitutions and indels","funder_award_id":"176316","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G896799909","display_name":null,"funder_award_id":"31003A_157064","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3210608097.pdf","grobid_xml":"https://content.openalex.org/works/W3210608097.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1866488244","https://openalex.org/W1970026646","https://openalex.org/W1996835973","https://openalex.org/W2017777683","https://openalex.org/W2024520916","https://openalex.org/W2044573154","https://openalex.org/W2067117360","https://openalex.org/W2074231493","https://openalex.org/W2087070363","https://openalex.org/W2092979861","https://openalex.org/W2096977241","https://openalex.org/W2110534451","https://openalex.org/W2120689690","https://openalex.org/W2127255727","https://openalex.org/W2127774996","https://openalex.org/W2150090955","https://openalex.org/W2214912059","https://openalex.org/W2256578114","https://openalex.org/W2541544080","https://openalex.org/W2890963022","https://openalex.org/W2962631801","https://openalex.org/W3096936098","https://openalex.org/W3103560422"],"related_works":["https://openalex.org/W4254318232","https://openalex.org/W2107335609","https://openalex.org/W3000366369","https://openalex.org/W2093169207","https://openalex.org/W1979486483","https://openalex.org/W2940885779","https://openalex.org/W2068647191","https://openalex.org/W2109676356","https://openalex.org/W3210608097","https://openalex.org/W2588053014"],"abstract_inverted_index":{"BACKGROUND:":[0],"Current":[1],"alignment":[2,42],"tools":[3],"typically":[4],"lack":[5],"an":[6,54,125],"explicit":[7,55,126],"model":[8,129],"of":[9,47,115,124,149,154],"indel":[10,25,127,184],"evolution,":[11],"leading":[12],"to":[13,21,131,134,143,192],"artificially":[14],"short":[15],"inferred":[16],"alignments":[17],"(i.e.,":[18],"over-alignment)":[19],"due":[20],"inconsistencies":[22],"between":[23],"the":[24,28,31,113,116,147,155,159,165],"history":[26],"and":[27,49,70,86,109,142,151,167,174],"phylogeny":[29],"relating":[30],"input":[32],"sequences.":[33],"RESULTS:":[34],"We":[35],"present":[36],"a":[37,74,138,178,182],"new":[38],"progressive":[39],"multiple":[40],"sequence":[41],"tool":[43],"ProPIP.":[44],"The":[45,63,77,90,99,122],"process":[46],"insertions":[48,150],"deletions":[50],"is":[51,65,71,92,102,110],"described":[52],"using":[53],"evolutionary":[56],"model-the":[57],"Poisson":[58],"Indel":[59],"Process":[60],"or":[61],"PIP.":[62],"method":[64],"based":[66],"on":[67,83,105],"dynamic":[68],"programming":[69],"implemented":[72,93],"in":[73,94,137,177,190],"frequentist":[75],"framework.":[76],"source":[78,100],"code":[79,101],"can":[80],"be":[81,188],"compiled":[82],"Linux,":[84],"macOS":[85],"Microsoft":[87],"Windows":[88],"platforms.":[89],"algorithm":[91],"C++":[95],"as":[96],"standalone":[97],"program.":[98],"freely":[103],"available":[104],"GitHub":[106],"at":[107],"https://github.com/acg-team/ProPIP":[108],"distributed":[111],"under":[112],"terms":[114],"GNU":[117],"GPL":[118],"v3":[119],"license.":[120],"CONCLUSIONS:":[121],"use":[123],"evolution":[128],"allows":[130],"avoid":[132],"over-alignment,":[133],"infer":[135,193],"gaps":[136],"phylogenetically":[139,194],"consistent":[140],"way":[141],"make":[144],"inferences":[145],"about":[146],"rates":[148],"deletions.":[152],"Instead":[153],"arbitrary":[156],"gap":[157,196],"penalties,":[158],"parameters":[160],"used":[161],"by":[162],"ProPIP":[163],"are":[164,175],"insertion":[166],"deletion":[168],"rates,":[169],"which":[170],"have":[171],"biological":[172],"interpretation":[173],"contextualized":[176],"probabilistic":[179],"environment.":[180],"As":[181],"result,":[183],"rate":[185],"settings":[186],"may":[187],"optimised":[189],"order":[191],"meaningful":[195],"patterns.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}