To be more clear, I have 3 different markers that are all mtDNA (D-loop, cytb and 12s rRNA). I used them for the same fish species and want to analyze them all together. If you have any papers on that, pls send me the link. WIll be nice to hear. Thanks!
There are many programs that allow to make "inferences" from several markers but they differ on the models that they implement and so the kind of "inferences" they can make. You need to be more specific on the question you intend to answer (inferring phylogeny? demography? gene flow?...). In any case, being the three markers from the mitochondrial chromosome there will be programs where you could concatenate the 3 markers to use them, since they will have the same genealogy. In other software (such as BEAST or IM), you have to specify for each gene if they are located in the same chromosome.
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