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Measuring Phylogenetic Information of Incomplete Sequence Data

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Cited 1 time in scopus

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dc.contributor.authorSeo, Tae-Kun-
dc.contributor.authorGascuel, Olivier-
dc.contributor.authorThorne, Jeffrey L.-
dc.date.accessioned2022-07-06T07:20:03Z-
dc.date.available2022-07-06T07:20:03Z-
dc.date.issued2022-04-19-
dc.identifier.urihttps://repository.kopri.re.kr/handle/201206/13542-
dc.description.abstractWidely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the effective sequence length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification. [Fisher information; gaps; insertion; deletion; indel; model adequacy; goodness-of-fit test; sequence alignment.]en_US
dc.languageEnglishen_US
dc.language.isoenen_US
dc.subjectEvolutionary Biologyen_US
dc.subject.classification기타()en_US
dc.titleMeasuring Phylogenetic Information of Incomplete Sequence Dataen_US
dc.title.alternativeGap이 포함된 DNA/아미노산 서열 데이터의 정보량 측정en_US
dc.typeArticleen_US
dc.identifier.bibliographicCitationSeo, Tae-Kun, Gascuel, Olivier, Thorne, Jeffrey L.. 2022. "Measuring Phylogenetic Information of Incomplete Sequence Data". <em>SYSTEMATIC BIOLOGY</em>, 71(3): 630-648.-
dc.citation.titleSYSTEMATIC BIOLOGYen_US
dc.citation.volume71en_US
dc.citation.number3en_US
dc.identifier.doi10.1093/sysbio/syab073-
dc.citation.startPage630en_US
dc.citation.endPage648en_US
dc.description.articleClassificationSCIE-
dc.description.jcrRateJCR 2020:6en_US
dc.subject.keywordMAXIMUM-LIKELIHOOD-ESTIMATIONen_US
dc.subject.keywordNUCLEOTIDE SUBSTITUTIONen_US
dc.subject.keywordEVOLUTIONARY INFERENCEen_US
dc.subject.keywordSTATISTICAL ALIGNMENTen_US
dc.subject.keywordMODEL SELECTIONen_US
dc.subject.keywordAMINO-ACIDen_US
dc.subject.keywordDNAen_US
dc.subject.keywordTREEen_US
dc.subject.keywordMITOCHONDRIALen_US
dc.subject.keywordBLOCKSen_US
dc.identifier.localId2022-0066-
dc.identifier.scopusid2-s2.0-85128493468-
dc.identifier.wosid000764687700001-
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