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. 2020 May 18;15:11. doi: 10.1186/s40793-020-00358-7

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© The Author(s) 2020, corrected publication 2024

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. 2 — The FRI workflow. 16S rRNA gene sequences are initially aligned against the reference sequences provided with Tax4Fun2 to identify the nearest neighbour. The OTU abundances for each sample are converted to presence-absence data and subsequently summarized based on the results from the nearest neighbour search. An association matrix (AM) containing the normalized functional profiles of those references identified in the 16S rRNA search is generated. The normalized functional profile in the AM is multiplied by the summarized OTU abundance. We assume that a function is present if the abundance of a function is greater than 50%. For instance, if 5 OTUs were affiliated to one 16S rRNA reference seqeunce, we would assume that every function with a minimum abundance of 10% in the normalized reference profile would be present in the AM. The FRI is finally calculated based on those community members possessing the function and their phylogenetic distribution. The amount of sequences/OTUs unused in the prediction (FSU/FTU) is provided in a log file 16S rRNA gene sequences are initially aligned against the reference sequences provided with Tax4Fun2 to identify the nearest neighbour. The presence of each OTU are summarized based on the results from the nearest neighbour search. An association matrix (AM) containing the functional profiles of those references identified in the 16S rRNA search is generated. The summarized abundances and the functional profiles stored in the AM are multiplied. Functions being present in all genomes are assumed to be present in the entire cluster. The functional redundancy is subsequently predicted from the average phylogenetic distance of all community members potentially possessing the function. This distance is subsequently normalized either by the average phylogenetic distance of the total reference tree (absolute) or by the distance found in the surveyed community (relative). FTU and FSU values are provided as a log file. The functions performing each step are marked with numbers