Supporting material and code for the primate comparative ACE2 project
Melin AD, Janiak MC, Marrone F, Arora PS, Higham JP. (2020). Comparative ACE2 variation and primate COVID-19 risk. Communications Biology, 3:641.
DOI: https://doi.org/10.1038/s42003-020-01370-w
Nucleotide sequences used in the study are available in the Alignments directory, or can be retrieved from NCBI with the script "fetch_ACE2_nucl_seqs.sh" using entrez direct utilities (https://www.ncbi.nlm.nih.gov/books/NBK179288/).
Sequences were translated, and aligned with MAFFT and manually inspected for variation at known key sites.
Gene trees were built with the scripts "ACE2_gene_tree_MrBayes.sh" and "ACE2_gene_tree_RAxML.sh."
Input and control files for all PAML codeml analyses are in the PAML directory.
Figures were made in RStudio using the R markdown file in the directory ACE2_Rcode.