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Adam, Kolyfetis et al., 2021. Supplementary Data.
Version 5 2022-08-19, 12:22
Version 4 2022-04-24, 16:30
Version 3 2022-04-22, 16:32
Version 2 2022-04-11, 11:09
Version 1 2021-08-01, 21:00
dataset
posted on 2021-08-01, 21:00 authored by Panagiotis AdamPanagiotis AdamCompressed Supplementary Data files for (Adam, Kolyfetis, et al., 2021). File descriptions are given below and in more detail in the readme file.
Supplementary Data 1
Data regarding all DUF phylogenies (taxonomic distributions, HMM profiles, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, phylogeny runs), plus local genome database records.
Supplementary Data 3
Supplementary Data 1
Data regarding all DUF phylogenies (taxonomic distributions, HMM profiles, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, phylogeny runs), plus local genome database records.
Supplementary Data 2
Data regarding methanogenesis markers phylogenies from (Borrel et al., 2019) (HMM profiles, DIAMOND seed sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs).
Supplementary Data 3
Data regarding congruence tests and the supermatrix phylogeny of Mcr.
Supplementary Data 4
Supplementary Data 4
Data regarding congruence tests and the supermatrix phylogeny of Mtr.
Supplementary Data 5
Supplementary Data 5
Data regarding the phylogenetic runs for the taxonomic placement of NRA7 (Archaeoglobi) and Bathyarchaeota metagenomic bins. Also data regarding AAI/ANI, biogeography, and 16S analyses, plus CheckM outfiles.
Supplementary Data 6
Supplementary Data 6
Data regarding the results of the metabolic prediction (BlastKOALA/dbCAN2/HydDB/MEROPS) for the genomes studied.
Supplementary Data 7
Supplementary Data 7
Data regarding methanogenesis marker phylogenies from (Gao & Gupta, 2007) and phylogenies of Wood-Ljungdahl pathway and methyltransferase proteins (HMM profiles, DIAMOND seed sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs).
Supplementary Data 8
Supplementary Data 8
Data regarding phylogenies of additional Eha, Ehb and Hcg proteins (HMM profiles, DIAMOND seed sequences, homology search outfiles with and without e-value threshold, alignments, trimmed alignments, and phylogeny runs).
Supplementary Data 9
Supplementary Data 9
Data regarding congruence tests and the supermatrix phylogenies of the Hcg proteins.
Supplementary Data 10
Data regarding congruence tests and the supermatrix phylogeny of Eha.
Supplementary Data 11
Supplementary Data 11
Data regarding congruence tests and the supermatrix phylogenies of Ehb.
Supplementary Data 12
Supplementary Data 12
Data regarding all rooting analyses on the supermatrices and the methyltransferases genes.
Supplementary Data 13
Supplementary Data 13
Data regarding gene and site concordance factor calculations for all supermatrices.
Supplementary Data 14
Supplementary Data 14
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.
Supplementary Data 15
Supplementary Data 15
Data regarding all Ancestral Sequence Reconstruction runs, homology searches of the ancestral sequences, trimmed ancestral sequences, and homology modeling of McrA.
