Supplementary Data for Kogay and Zhaxybayeva (2023)

<b>GTA head-tail cluster genes:</b><b>GTA_aln.zip: </b>Multiple sequence alignments of 14 GTA head-tail cluster genes selected to represent 293 OTUs. The alignments are in FASTA format.<b>GTA_uncstr_trees.zip: </b>Phylogenetic trees of 14 GTA head-tail cluster genes reconstructed under unconstrained topological search. The trees are in Newick format.<b>GTA_cstr_trees.zip: </b>Phylogenetic trees of 11 reference GTA genes, whose topology was constrained to match the reference phylogenomic tree. The trees are in Newick format.<b>Reference phylogenomic dataset:</b><b>reference_tree.zip: </b>Concatenated alignment of 84 phylogenetic marker genes found in 293 alphaproteobacterial genomes, in FASTA format (reference_tree_alignment.fasta). Reference phylogenomic tree reconstructed from the alignment, in Newick format (reference_tree_rooted.treefile).<b>1,470 alphaproteobacterial gene families:</b><b>OG_seq.zip: </b>Amino acid sequences of 1,470 gene families that are found in at least 50% of analyzed alphaproteobacterial genomes. The sequences are in FASTA format.<br><br><b>OG_cstr_trees.zip: </b>Phylogenetic trees of 1,470 gene families, whose topology was constrained to match the reference phylogenomic tree. The trees are in Newick format.<b>Evolutionary Rate Covariation analyses:</b><b>ERC_results_all.txt.zip: </b>Covariation of evolutionary rates for all pairwise gene comparisons of 11 reference GTA genes and 1,470 gene families.<b>Networks for </b><b><i>Phaeobacter inhibens</i></b><b>, </b><b><i>Caulobacter crescentus</i></b><b> and </b><b><i>Dinoroseobacter shibae</i></b><b>:</b><b>networks.zip: </b>co-evolutionary networks and their subnetworks of nodes with unambiguous GOG assignment, protein-protein interaction networks, fitness networks, and assignments of COG functional categories to nodes. Networks are in the “edge list” format.