I recently started my work for a university project where I want to analyze repetitive sequences in genomic DNA of two closely related species. I have no prior experience with this and have read some papers to start with.
I found there are a handful of programs for Tandem Repeat detection like TRF, Mreps, ATRhunter, RepeatMasker and so on. Based on different approaches and different opinions I could not really see a consensus in the articles I read on which program to use, not even on distinct (dis)advantages.
What I took away from them was, you have to be extra careful with your parameter settings for most of the programs and basically have to be author of the program to actually understand whats happening.
So I would like to hear opinions from people who actually use some kind of Repeat Detection software on this topic or have experience with the matter. Which programs you think are good? and where do you see their advantages or disadvantages?
PS: I am not sure this is the right place for this kind of "open" question so feel free to move it