There are many files created by the analysis pipeline. Salient files are listed here:

Genes that overlap sequences counted as a duplication by Sedef:

genes_in_resolved_dups.one_isoform.bed

Only one isoform per gene is retained here. The first 12 columns are the gene in bed12 format. Columns 13-15 are the coordinates of the first duplication, and columns 16-18 are the copy of the duplication.