ERCnet is meant to probe 'all-by-all' pairwise combinations of proteins. However, often times the proteome files that we input do not include plastid/mito-encoded proteins, meaning ERCnet analyses only include all pairwise combinations of nuclear-encoded proteins in practice. Since cyto-nuclear coevolution is often such an interesting angle, it would be helpful if ERCnet provided an easy way for the user to manually add plastid genes into the set of genes that ERCnet analyzes. I'm thinking this would be an argument at the Phylogenomics.py stage of the analysis. We've 'hacked' ERCnet to accomplish this before, so I'm thinking the feature we add will just make this type of 'hacking' easier.
ERCnet is meant to probe 'all-by-all' pairwise combinations of proteins. However, often times the proteome files that we input do not include plastid/mito-encoded proteins, meaning ERCnet analyses only include all pairwise combinations of nuclear-encoded proteins in practice. Since cyto-nuclear coevolution is often such an interesting angle, it would be helpful if ERCnet provided an easy way for the user to manually add plastid genes into the set of genes that ERCnet analyzes. I'm thinking this would be an argument at the Phylogenomics.py stage of the analysis. We've 'hacked' ERCnet to accomplish this before, so I'm thinking the feature we add will just make this type of 'hacking' easier.