I am currently dealing with the study of T.gondii's proteome. I downloaded the complete set of CDS from NCBI GenBank and I am now starting to decide how to implement the analysis. I'm pretty accostumed with Neutrality plot (Suoeka,1989) Pr2 plot (Sueoka,1995)and the Effective Number of Codons (Wright,1996) and now They are getting somewhat boring to implement since I largely used them. I have also experience with Kaks but I was wondering if there Is some index to distinguish between positive and negative selective pressure without a set of of reference genes.


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