SNP data to Phylogenetics

[crader]

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.

[jboone123]

Is there a ref genome available or a closely related one?

[crader]

Heya,

Its funky- we have the genome of a clade, where at least 2 exist. Its the earthworm, Lumbricus rubellus by the way, which consists of a species complex with huge variation (~13.5%).

In the meantime, I used the -g option in the "populations" programme of stacks (after denovo_map.pl with -s, as opposed to a super parent) and a series of filters to extract snps.

[rjohnp]

Hi,

I've been doing a similar thing. Depending on the format you have your SNPs in a custom Perl script worked a treat for me. I just concatenated them all into FASTA entries for each individual (from .VCF files in my case).