Thank you Sergei for your comments.
I am analyzing a set of sequences of VSV from different parts of Mexico, typically is say that VSV evolves over positive selective pressure but I am finding that negative is maybe more important. Other authors have used this site to calculate dN/d/S (SNAP/README) based on Nei and Gojobori (1986) method and they have find high values of positive selection. If I analyze my data in that web server I get the same. Could you tell me some differences between the use of this method and your methods.

2.- Based on the results by your methods could I conclude that negative selection plays a more important roll that positive. (my sample size is 138 from 5 years)

Thank you
Sincerely,
Lauro.