[Bioperl-l] Fu and Li's D statistic - calculate

Johri, Saurabh s.johri at imperial.ac.uk
Thu May 4 08:50:34 EDT 2006


Hi all,

I'm trying to calculate Fu and Li's D summary statistic for a group of
sequences.
the function fu_and_li_D(@ingroup,$extmutations)  takes 2 args, the
first being the ingroup (population) and the second being the number of
external mutations
which is calculated from an outgroup sequence.. 
 
my question is, which function do i use to calculate the number of
external mutations ?
would this be the singleton_count() function ?
the singleton_count() function takes a PopGen object - which represents
a clustal alignment file...
would i include the outgroup in a multiple fasta file for alignment with
clustal ?
 
any suggestions as to how to calculate the number of external mutations
would be much appreciated
 
Thanks for your help!
 


Saurabh Johri
Centre for Molecular Microbiology & Infection
Imperial College London
SW7 2AZ

 



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