This dataset contains genomes, proteomes and protein alignments mentioned in Hugoson et al (2021). It has been used to analyze the evolution of host-adaptation in the order Legionellales. The data is organized by dataset type, and then by dataset. The four datasets used here are Gamma105, comprising 105 Gammaproteobacteria and 5 outgroups; Legio93, comprising 93 Legionellales and 20 outgroups; Gamma66, derived from Gamma105 by removing Legionella, Francisella, Fangia and Piscirickettsia genera; Bacteria72, comprising 49 Gammaproteobacteria and 23 outgroups. 1_genomes Genomes as downloaded or assembled 1_1_Gamma105 1_2_Legio93 1_3_Gamma66 1_4_Bacteria72 2_proteomes Proteomes, as annotated by prokka 2_1_Gamma105 2_2_Legio93 2_3_Gamma66 2_4_Bacteria72 3_alignments In the first three folders, the following files are found. All sequence and alignment files are in fasta format: *_concatenated.fasta: concatenated alignment, trimmed. *.map: map of the files, tab-separated. The first row is a title row. The three first columns give the organism, the marker and the id (as found in the fasta file) for the protein. *_unaligned: non-aligned sequences for each marker. *_aligned: aligned sequences, for each marker. The prefix gives the software used for the alignment. *_trimmed: aligned, trimmed sequences for each marker. The prefix gives the software used to trim the alignment. 3_1_Gamma105: Based on the Bact109 set of marker, used in Figure 5 and Supplementary Figures 2, 7 and 12 3_2_Legio93: Based on the Bact109 set of marker, used in Figure 1 and Supplementary Figures 1, 2 and 11 3_3_TB4SS_auto: Alignment of 12 genes of the T4BSS, automatically detected in all genomes. Used for the tree in Supplementary Figure 5. 3_4_TB4SS_manual: Alignment of 25 genes of the T4BSS, manually curated by collinearity analysis. Used for the tree in Supplementary Figure 6. 3_5_Gamma66: Based on the Bact109 set of marker, used for the tree in Supplementary Figure 9. 3_6_Bacteria72: Based on the Bact109 set of marker, used for the tree in Supplementary Figure 10.