I am trying to characterize inter-specific divergence for DNA barcoding analysis. while on this, i uploaded sequences on MEGA and grouped but i am a bit confused with the grouping for average theta prime (theta prime is the mean distance within each genus). The question now is do i group by genera or by species to achieve this, Will i have the values recorded against each species or genus ?
Thanks
Dear Aramide,
In MEGA you can calculate between group and within group genetic distances and also pairwise distances. If you use pairwise distance options it will be calculated for each possible sequence pairs. If you use group distance than it depends on you, how to label each group. The software will designate a group by the common label. If you use genus group labelling (e.g. gen1, gen1....; gen2, gen2...; gen3, gen 3...) than you can calculate within and between genera distances. But you can designate e.g. species groups in similar way as well.
Thank you csaba for your answer, this was what I did initially. I grouped into genus for the interspecific distance and species for intra specific. This is a further confirmation. Thanks!!
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