I've downloaded package of LTR's in a specific organism from table browser, and i want to compare them between themselves in order finding missmatch mutations and to realize who is "older".
what is the right command?
blast is likely going to be step 1 indeed. But as I mention "step 1" you should realise that this is a process consisting of several steps. Moreover, "dating" LTRs is quite a specific analysis (though it can and has been done).
For more detailed info I suggest you google around, there are tools/pipelines/guidelines available on the internet explaining this. (if you are still stuck, then we would be happy to assist you further)
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