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basic population genetic statistics (Read 3413 times)
rbjmax
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basic population genetic statistics
Oct 25th, 2012 at 2:30pm
 
hi all-
I would like to calculate 'pi' for my virus populations- mean number of pairwise nucleotide differences weighted by numbers of individuals per haplotype. is this available in HyPhy?

thanks!
Rachel
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Sergei
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Re: basic population genetic statistics
Reply #1 - Oct 26th, 2012 at 11:18am
 
Hi Rachel,

How do you want to supply the # of individuals per haplotype? You could encode that in the sequence name, e.g.

>seq1_100
act...
>seq2_500
agt...

or by providing a separate file, such as

seq_name, haplotype_count
seq1,100
seq2,500

Sergei
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Division of Biomedical Informatics
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rbjmax
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Re: basic population genetic statistics
Reply #2 - Nov 7th, 2012 at 11:18am
 
Sergei-
I have both file types prepared. the first option is the most cohesive with my overall data management strategy.

Rachel
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Sergei
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Re: basic population genetic statistics
Reply #3 - Nov 13th, 2012 at 4:34pm
 
Hi Rachel,

Use the attached. It expects an alignment where each sequence id is like "tag_count", e.g. seq1_500

Sergei


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Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
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rbjmax
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Re: basic population genetic statistics
Reply #4 - Jan 4th, 2013 at 2:48pm
 
thank you, Sergei!

that .bf ran beautifully, thank you. does it utilize the Nei 1987 method like Arlequin used to? also, the values were about 100 times higher than I expected- are they percentage values?

Rachel
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Sergei
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Re: basic population genetic statistics
Reply #5 - Jan 4th, 2013 at 3:41pm
 
Hi Rachel,

The method is as simple as it gets: just compute the NUMBER of pairwise differences between sequences. It doesn't for example take sequence length into account, which is why you may be seeing numbers 100* larger that expected. The attached code implements the Nei and Li (1979) method (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login), which uses proportions.

Sergei
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Re: basic population genetic statistics
Reply #6 - Jan 7th, 2013 at 10:46am
 
perfect, thanks Sergei
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