To perform within-species comparison, we focused on paralogous groups resulting from the first step of orthology assignment (supplementary information online), after which 10,947 proteins were clustered in 3,761 paralogous groups (supplementary Table S2 online).
Associations of the vitamin D metabolites with IMT did not differ by sex or DCCT treatment assignment (Supplementary Table 5).
Associations of the vitamin D metabolites with CAC did not differ by sex or DCCT treatment assignment (Supplementary Table 5).
The majority of contigs under diversifying selection were found to be related to binding activity in the molecular function category of GO assignment (Supplementary Table S3).
ESRD was identified based on International Classification of Diseases, 9th revision (ICD-9 code assignment (Supplementary data, Table S1) or an estimated GFR (eGFR) <15 mL/min/1.73 m.
The 'reference dataset for COG (Cluster of Orthologous Groups of proteins) assignment' (Supplementary Table S2) contained 343 microbial genome sequences where COG assignment has been made for all the genes by the NCBI.
To get insights into the lactic acid fermentation characteristics of strain QU 25, we performed the comparative analysis on the presence of key enzymes related to lactic acid fermentation from xylose using KO (KEGG Orthology) gene assignment (Supplementary Table S5).
SPARKY (https://www.cgl.ucsf.edu/home/sparky) remains the most popular computer program for NMR operations, such as peak-picking and peak assignment (Supplementary Fig. S1), despite that fact that its originators have not released a new version since 2001 (Goddard and Kneller, 2008, SPARKY 3).
Using the prokaryotic 16S rDNA sequences from the Greengenes database (DeSantis et al. 2006), these sequences received the most accurate taxonomic assignment possible (supplementary table S4, Supplementary Material online).
The low macro-precision observed for CARMA3 and MEGAN4 is largely due to the prediction of many small bins with many false assignments (Supplementary Material, 'V. Performance measures').
We generated assignments with taxator-tk, CARMA3 and MEGAN4/5 under equivalent conditions, once with nucleotide and once separately with protein local alignments, and compared them with both Kraken and the published PhyloPythiaS assignments (Supplementary Fig. S21).
