Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability

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  • dc.contributor.author Chang, Jia-Ming, 1978-
  • dc.contributor.author Floden, Evan Wade
  • dc.contributor.author Herrero, Javier
  • dc.contributor.author Gascuel, Olivier
  • dc.contributor.author Di Tommaso, Paolo
  • dc.contributor.author Notredame, Cedric
  • dc.date.accessioned 2021-12-21T11:07:20Z
  • dc.date.available 2021-12-21T11:07:20Z
  • dc.date.issued 2019
  • dc.description.abstract Motivation: Most evolutionary analyses are based on pre-estimated multiple sequence alignment. Wong et al. established the existence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies. They were able to show that in many cases different aligners produce different phylogenies, with no simple objective criterion sufficient to distinguish among these alternatives. Results: We demonstrate that incorporating MSA induced uncertainty into bootstrap sampling can significantly increase correlation between clade correctness and its corresponding bootstrap value. Our procedure involves concatenating several alternative multiple sequence alignments of the same sequences, produced using different commonly used aligners. We then draw bootstrap replicates while favoring columns of the more unique aligner among the concatenated aligners. We named this concatenation and bootstrapping method, Weighted Partial Super Bootstrap (wpSBOOT). We show on three simulated datasets of 16, 32 and 64 tips that our method improves the predictive power of bootstrap values. We also used as a benchmark an empirical collection of 853 1-to-1 orthologous genes from seven yeast species and found wpSBOOT to significantly improve discrimination capacity between topologically correct and incorrect trees. Bootstrap values of wpSBOOT are comparable to similar readouts estimated using a single method. However, for reduced trees by 50% and 95% bootstrap thresholds, wpSBOOT comes out the lowest Type I error (less FP). Availability: The automated generation of replicates has been implemented in the T-Coffee package, which is available as open source freeware available from www.tcoffee.org. Supplementary information: Supplementary data are available at Bioinformatics online.
  • dc.description.sponsorship This work was supported by the Spanish Ministry of Science Plan Nacional [BFU2008-00419 to P.D.T. and C.N.]; the Wellcome Trust [WT095908 to P.F.]; the INCEPTION project [PIA/ANR-16-CONV-0005 to O.G.]; the Taiwan Ministry of Science and Technology [106-2221-E-004-011-MY2 to J.-M.C.]. We acknowledge support of the European Molecular Biology Laboratory, the Spanish Ministry of Economy and Competitiveness, “Centro de Excelencia Severo Ochoa 2013-2017” and “The Human Project from Mind, Brain and Learning” of NCCU from the Higher Education Sprout Project by the Ministry of Education in Taiwan
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Chang JM, Floden EW, Herrero J, Gascuel O, Tommaso PD, Notredame C. Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. Bioinformatics. 2019 Feb 6;37(11):1506-1514. DOI: 10.1093/bioinformatics/btz082
  • dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btz082
  • dc.identifier.issn 1367-4803
  • dc.identifier.uri http://hdl.handle.net/10230/51908
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2008-00419
  • dc.rights © Jia-Ming Chang et al. 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.other Filogènia
  • dc.subject.other Genètica
  • dc.title Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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