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Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-26176
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dc.contributor.authorJowkar, Gholamhossein-
dc.contributor.authorPecerska, Julija-
dc.contributor.authorMaiolo, Massimo-
dc.contributor.authorGil, Manuel-
dc.contributor.authorAnisimova, Maria-
dc.date.accessioned2022-11-25T10:13:36Z-
dc.date.available2022-11-25T10:13:36Z-
dc.date.issued2022-07-22-
dc.identifier.issn1063-5157de_CH
dc.identifier.issn1076-836Xde_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/26176-
dc.descriptionErworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)de_CH
dc.description.abstractModern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.de_CH
dc.language.isoende_CH
dc.publisherOxford University Pressde_CH
dc.relation.ispartofSystematic Biologyde_CH
dc.rightshttp://creativecommons.org/licenses/by-nc/4.0/de_CH
dc.subjectPoisson indel processde_CH
dc.subjectSARS-CoVde_CH
dc.subjectAncestral sequencede_CH
dc.subjectDynamic programmingde_CH
dc.subjectEvolutionary stochastic processde_CH
dc.subjectIndelde_CH
dc.subjectJoint ancestral sequence reconstructionde_CH
dc.subjectMaximum likelihoodde_CH
dc.subjectPhylogenyde_CH
dc.subject.ddc004: Informatikde_CH
dc.subject.ddc572: Biochemiede_CH
dc.titleARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel processde_CH
dc.typeBeitrag in wissenschaftlicher Zeitschriftde_CH
dcterms.typeTextde_CH
zhaw.departementLife Sciences und Facility Managementde_CH
zhaw.organisationalunitInstitut für Computational Life Sciences (ICLS)de_CH
dc.identifier.doi10.1093/sysbio/syac050de_CH
dc.identifier.doi10.21256/zhaw-26176-
dc.identifier.pmid35866991de_CH
zhaw.funding.euNode_CH
zhaw.issue2de_CH
zhaw.originated.zhawYesde_CH
zhaw.pages.end318de_CH
zhaw.pages.start307de_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume72de_CH
zhaw.publication.reviewPeer review (Publikation)de_CH
zhaw.funding.snf176316de_CH
zhaw.webfeedComputational Genomicsde_CH
zhaw.webfeedBiomedical String Analysisde_CH
zhaw.funding.zhawFrequentist estimation of the evolutionary history of sequences with substitutions and indelsde_CH
zhaw.author.additionalNode_CH
zhaw.display.portraitYesde_CH
zhaw.relation.referenceshttps://doi.org/10.5061/dryad.wstqjq2njde_CH
zhaw.relation.referenceshttps://github.com/acg-team/bpp-ARPIPde_CH
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Jowkar, G., Pecerska, J., Maiolo, M., Gil, M., & Anisimova, M. (2022). ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process. Systematic Biology, 72(2), 307–318. https://doi.org/10.1093/sysbio/syac050
Jowkar, G. et al. (2022) ‘ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process’, Systematic Biology, 72(2), pp. 307–318. Available at: https://doi.org/10.1093/sysbio/syac050.
G. Jowkar, J. Pecerska, M. Maiolo, M. Gil, and M. Anisimova, “ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process,” Systematic Biology, vol. 72, no. 2, pp. 307–318, Jul. 2022, doi: 10.1093/sysbio/syac050.
JOWKAR, Gholamhossein, Julija PECERSKA, Massimo MAIOLO, Manuel GIL und Maria ANISIMOVA, 2022. ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process. Systematic Biology. 22 Juli 2022. Bd. 72, Nr. 2, S. 307–318. DOI 10.1093/sysbio/syac050
Jowkar, Gholamhossein, Julija Pecerska, Massimo Maiolo, Manuel Gil, and Maria Anisimova. 2022. “ARPIP : Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process.” Systematic Biology 72 (2): 307–18. https://doi.org/10.1093/sysbio/syac050.
Jowkar, Gholamhossein, et al. “ARPIP : Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process.” Systematic Biology, vol. 72, no. 2, July 2022, pp. 307–18, https://doi.org/10.1093/sysbio/syac050.


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