Supplementary material for the manuscript "Covariation of Amino Acid Positions in HIV-1 Protease"

Data set File Comment
Untreated (notx) sequence set fasta format 648 unrelated nucleotide sequences in fasta format.
fasta format 648 unrelated amino acid sequences in fasta format.
Treated (tx) sequence set fasta format 531 unrelated nucleotide sequences in fasta format.
fasta format
 531 unrelated amino acid sequences in fasta format.
All four sequence files
 gzip archive
 gzip archive of all four files (UNIX line endings); expand using Stuffit Expander or the command:
tar xzvf hoffman_pro_seqs.gz

Please note that most of these sequences were obtained from the Stanford HIV Drug Resistance Database. Sets of "unrelated" sequeneces were generated using both epidemiological information available from the database, and using phylogenetic techniques described in the manuscript.