Adam, Kolyfetis et al., 2022. Supplementary Data.

Abstract

Compressed Supplementary Data files for (Adam, Kolyfetis, et al., 2022). File descriptions are given below and in more detail in the readme file. This is version 20220819. Data_S1 Data regarding all DUF phylogenies (taxonomic distributions, HMM profiles, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, phylogeny runs), plus lists of genomes in local databases. Data_S2 Data regarding methanogenesis markers phylogenies from (Borrel et al., 2019) (HMM profiles, DIAMOND query sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs). Data_S3 Data regarding methanogenesis marker phylogenies from (Gao & Gupta, 2007) and phylogenies of Wood-Ljungdahl pathway and methyltransferase proteins (HMM profiles, DIAMOND query sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs), plus SyntTax outputs. Data_S4 Data regarding congruence tests and the concatenation phylogeny of Mcr. Data_S5 Data regarding congruence tests and the concatenation phylogeny of Mtr. Data_S6 Data regarding phylogenies of additional Eha, Ehb and Hcg proteins (HMM profiles, DIAMOND query sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs). Data_S7 Data regarding congruence tests and the concatenation phylogeny of Eha. Data_S8 Data regarding congruence tests and the concatenation phylogenies of Ehb. Data_S9 Data regarding all rooting analyses on the concatenations and the methyltransferases genes. Data_S10 Data regarding gene and site concordance factor calculations for all concatenations. Data_S11 Data regarding all Ancestral Sequence Reconstruction runs, homology searches of the ancestral sequences, trimmed ancestral sequences, and homology modeling of McrA. Data_S12 Data regarding congruence tests and the concatenation phylogenies of the Hcg proteins. Data_S13 Data regarding site-specific rate calculations, benchmarks, and all related statistical tests. Transmembrane segment prediction runs and statistical tests for their relationship eith site-specific rates. Data_S14 Data regarding the phylogenetic runs for the taxonomic placement of NRA7 (Archaeoglobi) and Bathyarchaeia metagenomic bins. Also data regarding AAI/ANI, biogeography, and 16S analyses, plus CheckM outfiles. Data_S15 Data regarding the results of the metabolic prediction (BlastKOALA/dbCAN2/HydDB/MEROPS) for the genomes studied. Data_S16 Custom scripts (same as in the manuscript's Github repository, along with their license and readme file) and a file with the R functions (statistics) used in the analyses.