Quote:
Originally Posted by BioKiwi
Thanks pmiguel. Is mapping to organnells genome is a good option. I know that their size is smaller in comparison to nuclear genome, but they are available for some close relatives of the species.
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Yes. Also, for plant samples you can usually assemble the chloroplast from just a fraction of the data because of the high molar contribution of chloroplast DNA to most plant genomic DNA preps.
But mapping to a relative would likely work as well. Doesn't matter if there areas that don't map, these areas have no reason to create bias in inter-pair distance measurements.
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Phillip