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

vitis biojiangke at gmail.com
Tue Nov 8 17:51:22 EST 2011

If you read the Bio::PopGen doc, you'll see there is an optional argument for
the function that calculates pi, which is taking the number of sites into
consideration. Also, when you use the aln_to_population function to input an
alignment, you can use the option to take in all sites, including the
monomorphic sites. I think if you implement both in your script, you'll get
the same pi value as from other applications like DnaSP.

In terms of sliding window analyses, you may have to implement your own
method to move along the windows, but I think DnaSP is ready to do that, you
don't have to write your won script.

lvu.jun wrote:
> 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 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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