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. 2021 Jul 17;22:547. doi: 10.1186/s12864-021-07845-2

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Schematic view of the experimental designs supported by ARPEGGIO. There are 3 possible comparisons: a) polyploid species without assembly against its progenitors, b) same polyploid without assembly in two different experimental conditions and c) diploid species or polyploid species with an available phased assembly in two different experimental conditions. All comparisons are about whole genome DNA methylation patterns