I have a list of candidate genes as the result of my analysis. I am now trying to find various characteristics that they have in common. One of the things I would like to check is if my candidate genes are evolving faster or slower than the rest of the genes in my dataset.
Now, I know how to do this manually by building multi species alignments for each of my gene products and calculating ka/ks ratios for each set of alignments. This, however, is not a trivial process and I really do not want to do this manually for my ~1500 genes.
Can anyone suggest a tool that will take two lists of genes (or proteins) and return an estimate of evolutionary rate for each gene?