Data for "The heterogeneous selective landscape of genome evolution in prokaryotes"

The following repository contains data files to reproduce results described in "The heterogeneous selective landscape of genome evolution in prokaryotes". Aln_simulations_summary.txt - contains information of estimated and simulated (true) dN/dS and transition/transversion values. ATGC_COG_decomposition.out - contains results of decomposition analysis, including constraints and residuals. ATGC_COG_dnds_subtrees.tab - contains estimated dN/dS values of each subtree in splittable ATGCs. ATGC_COG_dnds_with_gaps.tab - contains dN/dS values, gaps per 1000 codons and length of alignments for all analyzed COGs across all ATGCs. atgc_genomes_list.txt - contains taxonomic information and assembly IDs of all analyzed genomes across 791 ATGCs. ATGC_splittable_bootstraps_estimates.out - contains transition/transversion and dN/dS estimates for bootstrapped codon alignments. Decomposed_COGs_categories.zip - contains tables with dN/dS values and decomposition results for analyzed COG groups. decomposition_code_local.pl - contains a script used to decompose ATGC-COG table into constraints and residuals. simulated_alns.zip - contains simulated alignments in FASTA format. summary_data.txt - contains summary information of various phylogenetic and genomic parameters for analyzed 791 ATGCs.