The average Ks value calculated for my set of sequences using MEGA6 (Modified Nei-Gojobori (NG96) method with Jukes Cantor correction) was 0.767.

The yn00 result from PAML however works out at 1.56

The results are really quite disparate - what is the reason for this difference, and is this normal?

I have double checked the input files and it all seems to be working correctly, so I have started to look at what a reasonable Ks value might be - I have seen references to sequences with Ks > 1 being unreliable for phylogenetic inference, but have also seen that for ML methods like yn00 some suggestions that Ks < 2 is fine.

This has made be question which result to go with, clearly different tools often give different results, but I would be grateful for your input as without the prior knowledge I am not sure what to go with.

Thanks