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Old 10-01-2014, 04:55 AM   #5
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Originally Posted by BioKiwi View Post
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.
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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