Thread: Correct use of Tajima D test?

Hi,

I have a question I hope somebody can help me with? When using Tajima D to test a bacterial gene for neutral evolution, should it just be used against all the novel alleles from a population, or all sequences of the gene from all isolates even if some are identical to each other? Does restricting to just the different alleles bias the results or is this how it is meant to be used?

I know that when looking at MLST allelic profiles for index of assocation values, both approcahes are used i.e analysis of just different profiles and analysis of all profiles from all isolates in the population.

many thanks

I'm sorry, i have not heard ever of a Tajima D test. My guess about the answer, is that it's probably dependent on the answer your trying to generate. Not sure if it's helpfull.