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• W4220791511 abstract "Molecular Ecology ResourcesVolume 22, Issue 3 p. 1228-1229 CORRIGENDUMFree Access This article corrects the following: pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data Katharine L. Korunes, Kieran Samuk, Volume 21Issue 4Molecular Ecology Resources pages: 1359-1368 First Published online: February 5, 2021 First published: 23 December 2021 https://doi.org/10.1111/1755-0998.13571AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat The article entitled “PIXY: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data” published in Molecular Ecology Resources (Volume 21, Issue 4, pages 1359-1368). In the original publication of this article, the algorithm shown in 1A and S1A is not consistent with the (correct) implementation of the algorithm for calculating mean nucleotide diversity in our software pixy. In both figures, the result in the second steps (“πraw”) should not be subsequently divided by the number of sites. We have confirmed that this inconsistency only exists in the schematic in Figures 1A and S1A and does not affect any other numerical results in the manuscript or those of the pixy software itself. We have included corrected versions of Figures 1 and S1 that depict the correct algorithm as implemented in the software. We thank Dr. Maciej Konopiński for identifying this error. FIGURE 1Open in figure viewerPowerPoint The logic and input/output of pixy demonstrated with a simple haploid example. (a) Comparison of two methods for computing π (or dXY) in the face of missing data. These methods follow the first expression of Equation (1) but differ in how they calculate the numerator and denominator. In Case 1, all missing data is assumed to be present but invariant. This results in a deflated estimate of π. In Case 2, missing data are simply omitted from the calculation, both in terms of the number of sites (the final denominator) and the component denominators for each site (the n choose two terms). This results in an unbiased estimate of π. (b) The adjusted π method (Case 2) as implemented for VCFs in pixy. The example VCF (input) contains the same four haplotypes as (a). Invariant sites are represented as sites with no ALT allele, and greyed-out sites are those that failed to pass a genotype filter requiring a minimum number of reads covering the genotype (Depth ≥ 10 in this case) Supporting Information Filename Description men13571-sup-0001-FigS1.pngPNG image, 102.9 KB Fig S1 Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. REFERENCE Korunes, K. L., & Samuk, K. (2021). PIXY: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources, 21(4), 1359– 1368. https://doi.org/10.1111/1755-0998.13326Wiley Online LibraryPubMedWeb of Science®Google Scholar Volume22, Issue3April 2022Pages 1228-1229 FiguresReferencesRelatedInformation" @default.
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