I need clarification regarding the input file (protein sequences) for accnet analysis. I have done roary pangenome analysis for my bacterial genomes (80 strains). Further, I would like to carryout accnet accessory clustering analysis, for which should I use accessory protein sequences generated by roary pangenome pipeline or should I consider the individual strains protein sequences obtained from prokka annotation pipeline.
I need clarification regarding the input file (protein sequences) for
accnetanalysis. I have doneroary pangenomeanalysis for my bacterial genomes (80 strains). Further, I would like to carryoutaccnetaccessory clustering analysis, for which should I use accessory protein sequences generated byroary pangenome pipelineor should I consider the individual strains protein sequences obtained fromprokkaannotation pipeline.