Heya,
I am trying to use RADseq for examining phylogeography in a similar manner to that of Emerson et al. (2010)
http://www.pnas.org/content/107/37/16196.full.pdf
An initial phylogeographic study is based upon Mt COII sequences, and then
individuals were pooled (n=3-6) and run through the RADseq protocol. I've then run them through the stacks pipeline.
http://creskolab.uoregon.edu/stacks/comp/denovo_map.php
I now have SNP data relative to a range of sites, but I'm not really sure what to do from here. I suppose I would like to compile a bunch of fasta sequences for phylogenetic analyses, constructed from positions where SNPs occur- but I'm not sure how to achieve this. If anyone can offer advice, I'd be eternally grateful!!
Cheers.
I am trying to use RADseq for examining phylogeography in a similar manner to that of Emerson et al. (2010)
http://www.pnas.org/content/107/37/16196.full.pdf
An initial phylogeographic study is based upon Mt COII sequences, and then
individuals were pooled (n=3-6) and run through the RADseq protocol. I've then run them through the stacks pipeline.
http://creskolab.uoregon.edu/stacks/comp/denovo_map.php
I now have SNP data relative to a range of sites, but I'm not really sure what to do from here. I suppose I would like to compile a bunch of fasta sequences for phylogenetic analyses, constructed from positions where SNPs occur- but I'm not sure how to achieve this. If anyone can offer advice, I'd be eternally grateful!!
Cheers.
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