Data for Weimann et al - Evolution and host-specific pathoadaptation of Pseudomonas aeruginosa

Additional data that was generated as part of this work, including clone trees, alignments, variants and accessory genome graph. Pairwise SNP distances between all patient representative and environmental samples (all_patient_dist_square.txt.gz) Variants that have occurred since the emergence of individual clone with detailed variant effects with variants due to recombination removed (all_mutations_wo_recomb.txt.gz) A summary of all single nucleotide variants that lead to amino acid changes with SIFT and FoldX predictions (all_aa_variants_info.txt.gz) Pseudogenome alignments for 155 individual clones (all_clones_aln.fasta.tar.gz) Clone trees inferred with Gubbins/RaxML (all_clones.nwk.tar.gz) BEAST input alignments for 21 epidemic clones (after pruning) (epidemic_clones_alignments_for_beast.fasta.tar.gz) BEAST input XMLs for 21 epidemic clones (lognormal/uniform/date randomisation test where applicable) (beast_xmls.tar.gz) BEAST combined trees for 21 epidemic clones (beast_trees.tar.gz) BEAST input XMLs for discrete trait phylogeographic analysis for 3 epidemic clones (beast_phylogeography.xmls.tar.gz) BEAST combined phylogeographic trees for 3 epidemic clones (phylogeography_trees.tar.gz) Cytoscape session file for Panaroo genome graph laid out and subset to ancestral genome representatives (ancestral_representatives_graph_layout.cys) Panaroo genome graph output based on all patient representative/environmental genomes (final_graph.gml.gz) Cytoscape session file for pathoadaptive STRING pathoadaptive gene-product network (pathoadaptive_gene_products_string_odds_ratio.cys)