mOTUs Tree (v4)

Phylogenetic tree of the mOTUs 4.0 species level clusters (mOTUs tool, mOTUs-db). Marker Selection and Pre-processing Phylogenetic reconstruction was performed separately for the bacterial and archaeal domains using a set of 10 universal marker genes extracted from the representative genomes (n=124'295) of the mOTUs database. Marker Set: The following Single Copy Marker genes were used: COG0012, COG0016, COG0018, COG0172, COG0215, COG0495, COG0525, COG0533, COG0541, and COG0552. Filtering: To prevent alignment artifacts caused by outliers (e.g., gene fusions or assembly errors), the top 1% longest sequences were removed from the dataset using a custom Python script prior to alignment. Alignment and Concatenation Alignment: Sequences were aligned using MAFFT (v7.505) with the --auto parameter. Trimming: Alignments were trimmed using trimAl (v1.4.rev15) with a gap threshold of 0.7 (-gt 0.7) Concatenation: The filtered individual gene alignments were concatenated into a single concatenate (one for each domain) using a custom Python script. Summary of Alignment Statistics: Metric Bacteria Archaea Total Genomes 120,445 3,850 Alignment Length 4,552 aa 4,811 aa Phylogenetic Inference Due to the vast difference in dataset size between the two domains, different inference strategies were employed to balance accuracy and computational efficiency. Bacteria (Approximate Maximum Likelihood) Given the large scale of the bacterial dataset (>120k genomes), the tree was inferred using FastTree (v2.1.11). Command parameters: -lg -gamma -fastest -noml Archaea (Maximum Likelihood) The archaeal dataset was processed using IQ-TREE 2 (v2.2.2.3), allowing for a more exhaustive Maximum Likelihood analysis. Command parameters: -m MFP -B 1000