Problem:
I have a list of candidate proteins 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 candidates are evolving faster or slower than the rest of the proteins in my dataset.
Now, I know how to do this manually by building multi species alignments for each of my proteins 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 candidates.
I am primarily interested in human but also mouse, yeast, fly and worm. Ideally, I would need a tool that can take a list of proteins, assign them to an orthologous group and return a value representing the rate of evolution for that group.
Can anyone suggest a tool that will take two lists of proteins and return an estimate of evolutionary rate for each one?