Assemblies_and_data_R1.zip

<b>All datasets used for the phylogenomics, phylogenetics, SSU rRNA tree, Virulency </b><b>factors, and HGTs.</b><br><b>Assemblies directory</b><b> contains:</b> two subdirectories: “full” contains raw rnaSPAdes v3.13 assemblies,“cleaned_based_on_taxonomy” contains decontaminated protein assemblies.<b>HGTs,</b><b> </b><b>Energy_generation_and_pyruvate_metabolism</b><b>, a</b><b>nd Virulency_factors</b><b> directories contain:</b> three subdirectories: “initial_fastas”, “final_fastas”, and “trees” respectively. The “initial_fasta” directory contains all the candidate sequences from the preliminary datasets. The “final_fastas” directory comprises of all sequenced after manual inspection and removal of xenolog sequences. Final trees in newick format are in the “trees” directory.<b>The SSUrRNA directory contains:</b> fasta file with all the SSU rRNA sequences (SSU_rRNA.fas) and the tree in newick format (SSU_rRNA.tre).<b>The Phylogenomics directory contains: </b>all the proteomes, single gene datasets, including all considered sequences (orthologs and paralogs), table with the information whether the gene was used in the final phylogenomic dataset or not as well as the information about taxon completeness (Taxon_Completness_Table.docx), and the table providing information about the source of the data, datatype and the taxonomical assignment of the data used for the phylogenomics (metadata.tsv).<b>The Phylogentics directory contains:</b> all the datasets used for the 4-gene phylogeny: single gene alignments (HSP90_concat.fasta, elonfation_factor_1_concat.fasta, alpha_tubulin_concat.fasta, SSU_rRNA_concat.fasta), final concatenated alignment (4-gene-phylogeny.aln) and final tree in newick format (4-gene-phylogeny.newick).<br>