Investigating amino acid distance measures in molecular evolution models, and proposing a new consensus measure

Key datafiles for the manuscript entitled "DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling" by Gavin Douglas and Louis-Marie Bobay. The key table most readers will be interested in is "all_distance_measures_symmetric.tsv.gz". This is tab-delimited table with the pairwise amino acid distances based on all the measures we evaluated. Each row corresponds to a different amino acid pair, but note that the distances are symmetric for all measures (i.e., those with asymmetric distances between amino acids were averaged to be symmetric). The final columns in this table that indicate combined measures with "+" are non-focal DISTATIS consensus measures. These subdirectories are in the compressed folder called "workflow_files", and contain the key files for running our analyses: aa_metrics - Working files for processing and analyzing AA distance/similarity measures. Note that those interested in the final measures should use "all_distance_measures_symmetric.tsv.gz" allele_freq_vs_predicted_effects - Key files used for analyzing segregating non-synonymous polymorphisms. PAML_workflow - Files for fitting codon substitution models with PAML proteinGym - Files from the proteinGym database used for producing the custom DMS-EX measure.