Multiple Hits per Gene

[emilyhyde]

Hello! I am running KoFamScan on a large dataset and I am getting 10+ hits on each gene (predicted with Prodigal) almost universally across my data. From the documentation, I cannot find a way to filter automatically for a top hit. Is this normal and post-run filtering is required or am I setting up my run incorrectly? Thank you very much in advance!