{"id":"https://openalex.org/W1966875588","doi":"https://doi.org/10.1142/s0219720006002168","title":"ON THE INFERENCE OF PARSIMONIOUS INDEL EVOLUTIONARY SCENARIOS","display_name":"ON THE INFERENCE OF PARSIMONIOUS INDEL EVOLUTIONARY SCENARIOS","publication_year":2006,"publication_date":"2006-06-01","ids":{"openalex":"https://openalex.org/W1966875588","doi":"https://doi.org/10.1142/s0219720006002168","mag":"1966875588","pmid":"https://pubmed.ncbi.nlm.nih.gov/16960972"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720006002168","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720006002168","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","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/A5065939739","display_name":"Leonid Chindelevitch","orcid":"https://orcid.org/0000-0002-6619-6013"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"LEONID CHINDELEVITCH","raw_affiliation_strings":["School of Computer Science, McGill University, 3480 University Street, Montreal, Quebec, H3A 2A7, Canada"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, 3480 University Street, Montreal, Quebec, H3A 2A7, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101926349","display_name":"Zhentao Li","orcid":"https://orcid.org/0000-0001-7178-033X"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"ZHENTAO LI","raw_affiliation_strings":["School of Computer Science, McGill University, 3480 University Street, Montreal, Quebec, H3A 2A7, Canada"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, 3480 University Street, Montreal, Quebec, H3A 2A7, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000042413","display_name":"Eric Blais","orcid":"https://orcid.org/0009-0000-5824-9034"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"ERIC BLAIS","raw_affiliation_strings":["McGill Centre for Bioinformatics and School of Computer Science, McGill University, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada"],"affiliations":[{"raw_affiliation_string":"McGill Centre for Bioinformatics and School of Computer Science, McGill University, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065720651","display_name":"Mathieu Blanchette","orcid":"https://orcid.org/0000-0002-9555-860X"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"MATHIEU BLANCHETTE","raw_affiliation_strings":["McGill Centre for Bioinformatics and School of Computer Science, McGill University, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada"],"affiliations":[{"raw_affiliation_string":"McGill Centre for Bioinformatics and School of Computer Science, McGill University, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5065939739"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":null,"apc_paid":null,"fwci":1.1921,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.75525681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"04","issue":"03","first_page":"721","last_page":"744"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9954000115394592,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.8309996724128723},{"id":"https://openalex.org/keywords/divide-and-conquer-algorithms","display_name":"Divide and conquer algorithms","score":0.5970495343208313},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5364101529121399},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5056312084197998},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.501509428024292},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47794440388679504},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4629918038845062},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4168599545955658},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4095565378665924},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3644775152206421},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3611775040626526},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.293687105178833},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24872499704360962},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22859546542167664},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.16117072105407715},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13853389024734497},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08143016695976257}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8309996724128723},{"id":"https://openalex.org/C71559656","wikidata":"https://www.wikidata.org/wiki/Q671298","display_name":"Divide and conquer algorithms","level":2,"score":0.5970495343208313},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5364101529121399},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5056312084197998},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.501509428024292},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47794440388679504},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4629918038845062},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4168599545955658},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4095565378665924},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3644775152206421},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3611775040626526},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.293687105178833},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24872499704360962},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22859546542167664},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.16117072105407715},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13853389024734497},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08143016695976257},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"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/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":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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019005","descriptor_name":"Cystic Fibrosis Transmembrane Conductance Regulator","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019005","descriptor_name":"Cystic Fibrosis Transmembrane Conductance Regulator","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019005","descriptor_name":"Cystic Fibrosis Transmembrane Conductance Regulator","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053476","descriptor_name":"Extinction, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720006002168","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720006002168","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:16960972","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16960972","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1544463887","https://openalex.org/W1608071358","https://openalex.org/W1872483787","https://openalex.org/W1963547452","https://openalex.org/W1966327236","https://openalex.org/W1968143987","https://openalex.org/W1971926406","https://openalex.org/W1984195830","https://openalex.org/W1987187756","https://openalex.org/W2057998009","https://openalex.org/W2069787595","https://openalex.org/W2095824228","https://openalex.org/W2100440346","https://openalex.org/W2102424972","https://openalex.org/W2112132489","https://openalex.org/W2151464048","https://openalex.org/W2155237411","https://openalex.org/W2166444569","https://openalex.org/W2254458779","https://openalex.org/W2505968561","https://openalex.org/W4254717640","https://openalex.org/W4293860921","https://openalex.org/W4301808069"],"related_works":["https://openalex.org/W3014493306","https://openalex.org/W4247744373","https://openalex.org/W2949462032","https://openalex.org/W2014270275","https://openalex.org/W2100983360","https://openalex.org/W4290667473","https://openalex.org/W3210055897","https://openalex.org/W2097020631","https://openalex.org/W2748610681","https://openalex.org/W2803360717"],"abstract_inverted_index":{"Given":[0],"a":[1,9,21,46,111,124,142],"multiple":[2],"alignment":[3],"of":[4,19,25,30,49,52,86,144],"orthologous":[5,148],"DNA":[6],"sequences":[7,149],"and":[8,27,56,98,136,139],"phylogenetic":[10],"tree":[11],"for":[12],"these":[13],"sequences,":[14],"we":[15,77],"investigate":[16],"the":[17,32,36,41,50,72,83,99,151],"problem":[18,51,73],"reconstructing":[20],"most":[22,105],"parsimonious":[23],"scenario":[24],"insertions":[26],"deletions":[28],"capable":[29],"explaining":[31],"gaps":[33],"observed":[34],"in":[35,96,104,150],"alignment.":[37],"This":[38],"problem,":[39],"called":[40],"Indel":[42],"Parsimony":[43],"Problem,":[44],"is":[45,74,94],"crucial":[47],"component":[48],"ancestral":[53],"genome":[54,64],"reconstruction,":[55],"its":[57],"solution":[58],"provides":[59],"valuable":[60],"information":[61],"to":[62,118],"many":[63],"functional":[65],"annotation":[66],"approaches.":[67],"We":[68,109],"first":[69],"show":[70],"that":[71,114],"NP-complete.":[75],"Second,":[76],"provide":[78],"an":[79,87],"algorithm,":[80],"based":[81],"on":[82,123,141],"fractional":[84],"relaxation":[85],"integer":[88],"linear":[89],"programming":[90],"formulation.":[91],"The":[92],"algorithm":[93],"fast":[95],"practice,":[97],"solutions":[100],"it":[101,116],"produces":[102],"are,":[103],"cases,":[106],"provably":[107],"optimal.":[108],"describe":[110],"divide-and-conquer":[112],"approach":[113],"makes":[115],"possible":[117],"solve":[119],"very":[120],"large":[121],"instances":[122],"simple":[125],"desktop":[126],"machine,":[127],"while":[128],"retaining":[129],"guaranteed":[130],"optimality.":[131],"Our":[132],"algorithms":[133],"are":[134],"tested":[135],"shown":[137],"efficient":[138],"accurate":[140],"set":[143],"1.8":[145],"Mb":[146],"mammalian":[147],"CFTR":[152],"region.":[153]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
