I have a data set of 700 coding sequences (which I saved in a reference.fa file) and I need to obtain the orthology relationships (orthologous and paralogous) of these genes against 70 species. I have downloaded the genome cds from NCBI for each species. Now, is it possible to get only these comparisons without going through the all vs all phase? Could I start OMA without comparing all the genomes (cds) with each other? How do I launch these analyses ?
Thanks for your help,