This Supplementary Material section consists of the following files (plus others below): 

- list.eukaryotes.txt                 
- list.prokaryotes_reference.txt
- list.prokaryotes_full.txt

These contain the list of species whose genome was searched in this paper. The prokaryotes_reference is a subset of 223 species prokaryotes_full (whose total is 8263), defined at NCBI as a "small curated subset of really good and scientifically important prokaryotic genomes". The files contain one species name per line; strange characters are masked to avoid problems during computation. 
This file: 

- names_and_taxids.tab

allows to get back to the original entry at ncbi taxonomy. It contains three columns separated by tab characters: species name (as in the files listed above); species name unmasked;  ncbi taxonomy id. 
The following alignment files:

- SPS.eukaryotes.fa
- SPS.prokaryotes.reference.fa
- SPS.prokaryotes.full.fa

contain the aligned, filtered predictions for SPS/SelD proteins found in those genomes. Format is fasta aligned. The fasta headers contain also information about the genomic coordinates in the target genome.
The following files:

- markers.prokaryotes_reference.tab
- markers.prokaryotes_full.tab

contain the list of Se utilization markers found in each one of the prokaryotic species, for each species in the two sets. See their first line for a description of each column.
The files:

- evolutionary.insects.fa
- evolutionary.vertebrata.fa
- evolutionary.summary_set.fa

contain the alignment of coding sequences used for evolutionary analysis (see Supplementary Material S5). The file:

- evolutionary.trees.txt

contains the gene trees for each of the sets above, in newick format