<p>Dear all, I would like to know if there is any statistical test / program that allows me check whether the third codon position in my alignment is evolving too fast (too divergent) that it should not be included in a phylogenetic analysis. I googled around and didn&#39;t get any hits. I appreciate if you can share what you know on this topic.</p>

There are a couple of tests for this, including Xia (2003, http://dx.doi.org/10.1016/S1055-7903(02)00326-3), which I gather is implemented in DAMBE.

Probably the most common way to asses this though, is to plot the number of 3rd codon substitutions in a sequence against some corrected distance . If the curve "plateaus" you know you are hitting saturation.