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So I have a project student (undergraduate) who has been assigned a project to study the evolution of a gene (and possibly related genes) through species. I am not an evolutionary biologist, and hence am not too experienced in the workflow usually followed in studying the evolution of a gene in molecular phylogenetics. I have a brief idea, but may be wrong, and hence please do correct me.

The first aim is obviously sequence data collection for the requisite gene (and a few for a good outgroup), plot them in a phylogenetic tree, and analyse the distances, Ka and Ks ratio.

The next logical thing in my mind was a simple data collection for SNP analysis, and see if the SNP's are conserved, across species, and possibly if they impact protein structure.

But that's where i draw a blank. Any other ideas?

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Uh naw snps shouldn't be first; snps are later –  caseyr547 Jul 28 '14 at 23:58
First should be clustering homologous Regions with clustalx and the like then measuring the distance between major regions....regions can be identified with hmm software like the nncbi conserved domain software –  caseyr547 Jul 28 '14 at 23:59
Read my friend Matt olsons ttu. papers his evolutionary work should provide a good guide –  caseyr547 Jul 29 '14 at 0:05
The snp idea is fine but it does betray your work in Molecular as that was my first suggestion to Matt –  caseyr547 Jul 29 '14 at 0:06
en.m.wikipedia.org/wiki/Ka/Ks_ratio#Individual_codon_approach do you mean like this? –  caseyr547 Jul 30 '14 at 21:12