You can calculate these parameters with the DNASP program available at
In article <7oa5ds$hik at net.bio.net>, mjcann at med.cornell.edu says...
>>I wish to calculate values for nucleotide polymorphism (theta) and
>nucleotide diversity (pi). Does anyone know of a nice freeware program
>that will do it for me. If not, what is the easiest way of going from
>DNA sequence to lovely numbers!?
>>Many thanks for your help
>>Department of Pharmacology
>Weill Medical College of Cornell University
>>e-mail: mjcann at med.cornell.edu>