FASTA file of the alignment underlying the phylogenetic tree that appears in Figure 3 of Santoro et al. 2019. The alignment is constructed from 32 concatenated proteins from 1360 archaeal genomes, including metagenome-assembled genomes, single-cell genomes, and cultivated isolates obtained from NCBI GenBank and the Joint Genome Institute's Integrated Microbial Genomes (IMG) portal. Phylogenetic markers were selected using hmmsearch against AMPHORA2 markers.