Molecular Clocks | Tajima’s Relative Rate Test
Use this to conduct Tajima’s relative rate test (Tajima 1993), which works in the following way. Consider three sequences, 1, 2 and 3, and let 3 be the out-group. Let nijk be the observed number of sites in which sequences 1, 2 and 3 have nucleotides i, j and k. Under the molecular clock hypothesis, E(nijk) = E(njik) irrespective of the substitution model and whether or not the substitution rate varies with the site. If this hypothesis is rejected, then the molecular clock hypothesis can be rejected for this set of sequences.
In response to this command, you can select the three sequences for conducting Tajima’s test. For nucleotide sequences, this test offers the flexibility of using only transitions, only transversions, or both. If the data is protein coding, then you can choose to analyze translated sequences or any combination of codon positions by clicking on the ‘Data for Analysis’ button.
See Nei and Kumar (2000) (page 193-196) for further description and an example.