I have used RepeatMasker to get repeats on different fasta files and have got multiple output files (out files). My aim is to find common repeats present in all output files and also the unique repeats present in each output file. Do you know any software that can do this?
The output files are too big for this to be done manually. I can try to write some script to do this but thought to ask first, if a software already exists for this task, to avoid reinventing the wheel.