What is a good tool to make saturation analyses?
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BBMap has a tool for that purpose:
bbcountunique.sh in=reads.fq out=hist.txt
or
bbcountunique.sh in=r1.fq in2=r2.fq out=hist.txt
You can plot the histogram with Excel. It tells you the percent of unique reads encountered as you go through the file, so the number steadily drops and ultimately reaches zero at 100% saturation (though in practice this rarely happens due to errors).
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Brian Bushnell
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What do you mean? Are you talking about mutation saturation between species? Or are you talking about sequencing saturation, i.e., estimating if you sequenced enough?
I'm talking about mutation saturation
In that case, I think my previous answer is probably wrong. But it would be helpful if you could elaborate your question a bit to provide additional detail.
Please, read Tutorial: How To Ask Good Questions On Technical And Scientific Forums, and spend some time and effort when asking your questions. We shouldn't have to guess what you want, it should be clear from your question.