I'm doing the phylogeography of a species and I'm trying to use nuclear markers in addition to cpDNA. I did a little research and found two good candidate regions for amplification, but I wanted to design primers that have a very good chance at amplifying in this species. I searched GenBank and found that no plants in the family of this species have any sequence data published for this region, so my best bet might be to search for other closely related families and aligning sequences for them. However, what I wanted to know is how to go about doing this. I mean, do I copy all nucleotide sequences from GenBank accessions and try aligning them with Mega? Or is there a better/more efficient method for doing this?
And what about primer design software? Which one(s) do you use and recommend?
Thank you in advance!