[Bioperl-l] questions about the bioperl module Bio::PopGen::Statistics

[lvu.jun]

Hi, there,
I am trying to calculate the population genetics parameters such as pi using the bioperl module Bio::PopGen::Statistics. But I found that the method only requires the input of the marker genotype of every individuals for the population. I don't know why the module does not take the DNA sequence length into consideration when calculating the pi value. According to the definition of the pi value, besides the polymorphic sites, we also need the monomorphic sites that should be incorporated in the denominator when doing the calculation. Is it right? therefore I'm confused about the module, who can tell me why it can correctly calculate the pi value only with the marker(polymorphic) genotype?
Another question, if I want to calculate the pi value using the sliding window along the genome, how can I do this using the Bio::PopGen::Statistics module?
Thanks for your help!
Yours sincerely,
Jun

Chinese Academy of Sciences

2011-06-01 



lvu.jun