{"id":"https://openalex.org/W2419892282","doi":"https://doi.org/10.1186/s12859-016-1077-7","title":"Evaluation of properties over phylogenetic trees using stochastic logics","display_name":"Evaluation of properties over phylogenetic trees using stochastic logics","publication_year":2016,"publication_date":"2016-06-14","ids":{"openalex":"https://openalex.org/W2419892282","doi":"https://doi.org/10.1186/s12859-016-1077-7","mag":"2419892282","pmid":"https://pubmed.ncbi.nlm.nih.gov/27301397"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1077-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1077-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1077-7","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/s12859-016-1077-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080044871","display_name":"Jos\u00e9 Ignacio Requeno","orcid":"https://orcid.org/0000-0001-5111-8357"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jos\u00e9 Ignacio Requeno","raw_affiliation_strings":["Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ Mar\u00eda de Luna 1, Zaragoza, 50018, Spain. nrequeno@unizar.es","Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ Mar\u00eda de Luna 1, Zaragoza, 50018, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ Mar\u00eda de Luna 1, Zaragoza, 50018, Spain. nrequeno@unizar.es","institution_ids":["https://openalex.org/I255234318"]},{"raw_affiliation_string":"Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ Mar\u00eda de Luna 1, Zaragoza, 50018, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066803149","display_name":"Jos\u00e9 Manuel Colom","orcid":"https://orcid.org/0000-0001-5066-4030"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Manuel Colom","raw_affiliation_strings":["Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ Mar\u00eda de Luna 1, Zaragoza, 50018, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Systems Engineering (DIIS), Universidad de Zaragoza, C/ Mar\u00eda de Luna 1, Zaragoza, 50018, Spain","institution_ids":["https://openalex.org/I255234318"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5080044871"],"corresponding_institution_ids":["https://openalex.org/I255234318"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3206,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.66129443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"17","issue":"1","first_page":"235","last_page":"235"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3000999987125397,"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":0.3000999987125397,"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":0.14059999585151672,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.08820000290870667,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/probabilistic-logic","display_name":"Probabilistic logic","score":0.7026874423027039},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6382757425308228},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5738092660903931},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5436469912528992},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5414050221443176},{"id":"https://openalex.org/keywords/model-checking","display_name":"Model checking","score":0.47626039385795593},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.46400490403175354},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41870805621147156},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38317960500717163},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3123042583465576},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22091510891914368},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15005266666412354},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11723524332046509}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.7026874423027039},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6382757425308228},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5738092660903931},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5436469912528992},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5414050221443176},{"id":"https://openalex.org/C110251889","wikidata":"https://www.wikidata.org/wiki/Q1569697","display_name":"Model checking","level":2,"score":0.47626039385795593},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.46400490403175354},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41870805621147156},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38317960500717163},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3123042583465576},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22091510891914368},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15005266666412354},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11723524332046509},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-016-1077-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1077-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1077-7","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:27301397","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27301397","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:europepmc.org:3875608","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4908722","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:zaguan.unizar.es:56183","is_oa":true,"landing_page_url":"http://zaguan.unizar.es/record/56183","pdf_url":null,"source":{"id":"https://openalex.org/S4306402461","display_name":"Zaguan (Universidad de Zaragoza)","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1077-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1077-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1077-7","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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2419892282.pdf","grobid_xml":"https://content.openalex.org/works/W2419892282.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W34141764","https://openalex.org/W420957490","https://openalex.org/W1498432697","https://openalex.org/W1516256348","https://openalex.org/W1547246349","https://openalex.org/W1862398452","https://openalex.org/W1969042907","https://openalex.org/W1970429135","https://openalex.org/W1990607929","https://openalex.org/W2005998857","https://openalex.org/W2020968244","https://openalex.org/W2026062398","https://openalex.org/W2036614038","https://openalex.org/W2053726896","https://openalex.org/W2071465766","https://openalex.org/W2094063883","https://openalex.org/W2094494177","https://openalex.org/W2097697760","https://openalex.org/W2102424972","https://openalex.org/W2107701089","https://openalex.org/W2110062879","https://openalex.org/W2114671730","https://openalex.org/W2117055771","https://openalex.org/W2117189826","https://openalex.org/W2117752525","https://openalex.org/W2118820512","https://openalex.org/W2141052558","https://openalex.org/W2150934173","https://openalex.org/W2155836971","https://openalex.org/W2159032237","https://openalex.org/W2163892779","https://openalex.org/W2164096878","https://openalex.org/W2184948333","https://openalex.org/W2340735175","https://openalex.org/W2368443971","https://openalex.org/W2506987745","https://openalex.org/W2749566243","https://openalex.org/W2911733266","https://openalex.org/W2913459036","https://openalex.org/W2978698603","https://openalex.org/W3193351719","https://openalex.org/W4230357098","https://openalex.org/W4233815609","https://openalex.org/W4244797807","https://openalex.org/W4248079778","https://openalex.org/W6684644128"],"related_works":["https://openalex.org/W4312203868","https://openalex.org/W2069013776","https://openalex.org/W2059637021","https://openalex.org/W2038264393","https://openalex.org/W2378282666","https://openalex.org/W4210644918","https://openalex.org/W2362218761","https://openalex.org/W2062354928","https://openalex.org/W2113708670","https://openalex.org/W2088120817"],"abstract_inverted_index":{"BACKGROUND:":[0],"Model":[1],"checking":[2,161,219,243,275],"has":[3,116],"been":[4,117],"recently":[5],"introduced":[6],"as":[7,21,53,62,145],"an":[8,25],"integrated":[9],"framework":[10,137,247],"for":[11,77,138,229,248],"extracting":[12],"information":[13,143],"of":[14,27,33,40,56,73,123,134,159,168,192,203,233,266,273,288,297,302],"the":[15,51,96,98,103,124,132,135,190,213,217,227,231,264,271,278,282,293,300],"phylogenetic":[16,43,255],"trees":[17],"using":[18],"temporal":[19],"logics":[20,29,74],"a":[22,34,38,47,54,81,87,108,166,172,193,198,245,289],"querying":[23],"language,":[24],"extension":[26],"modal":[28],"that":[30,65,90,110,181,240],"imposes":[31],"restrictions":[32],"boolean":[35],"formula":[36],"along":[37],"path":[39],"events.":[41],"The":[42],"tree":[44,194],"is":[45,105,244],"considered":[46,119],"transition":[48],"system":[49],"modeling":[50],"evolution":[52],"sequence":[55],"genomic":[57],"mutations":[58],"(we":[59],"understand":[60],"mutation":[61,199],"different":[63],"ways":[64],"DNA":[66],"can":[67],"be":[68,183],"changed),":[69],"while":[70],"this":[71,114,128,151],"kind":[72],"are":[75],"suitable":[76],"traversing":[78],"it":[79],"in":[80,171,209],"strict":[82],"and":[83,140,175,250,261,268,286],"exhaustive":[84],"way.":[85],"Given":[86],"biological":[88],"property":[89],"we":[91,130,153,176,188,205,224],"desire":[92],"to":[93,162,197,211,263,292],"inspect":[94],"over":[95,120,254],"phylogeny,":[97],"verifier":[99],"returns":[100],"true":[101],"if":[102],"specification":[104],"satisfied":[106],"or":[107,148],"counterexample":[109],"falsifies":[111],"it.":[112],"However,":[113],"approach":[115],"only":[118],"qualitative":[121,169],"aspects":[122],"phylogeny.":[125],"RESULTS:":[126],"In":[127,222],"paper,":[129],"repair":[131],"limitations":[133],"previous":[136],"including":[139],"handling":[141],"quantitative":[142,252],"such":[144],"explicit":[146],"time":[147],"probability.":[149],"To":[150],"end,":[152],"apply":[154],"current":[155],"probabilistic":[156,241],"continuous-time":[157],"extensions":[158],"model":[160,218,242,274],"phylogenetics.":[163],"We":[164,237],"reinterpret":[165],"catalog":[167],"properties":[170,180,253],"numerical":[173],"way,":[174],"also":[177],"present":[178],"new":[179],"couldn't":[182],"analyzed":[184],"before.":[185],"For":[186],"instance,":[187],"obtain":[189,212],"likelihood":[191,215],"topology":[195],"according":[196],"model.":[200],"As":[201],"case":[202],"study,":[204],"analyze":[206],"several":[207],"phylogenies":[208],"order":[210],"maximum":[214,234],"with":[216],"tool":[220,291],"PRISM.":[221],"addition,":[223],"have":[225,238],"adapted":[226],"software":[228,290],"optimizing":[230],"computation":[232],"likelihoods.":[235],"CONCLUSIONS:":[236],"shown":[239],"competitive":[246],"describing":[249],"analyzing":[251],"trees.":[256],"This":[257],"formalism":[258],"adds":[259],"soundness":[260],"readability":[262],"definition":[265],"models":[267],"specifications.":[269],"Besides,":[270],"existence":[272],"tools":[276],"hides":[277],"underlying":[279],"technology,":[280],"omitting":[281],"extension,":[283],"upgrade,":[284],"debugging":[285],"maintenance":[287],"biologists.":[294],"A":[295],"set":[296],"benchmarks":[298],"justify":[299],"feasibility":[301],"our":[303],"approach.":[304]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
