Dear all,

Apparently, several collaegues cope with the question how one can 
correct for sample sizes, when analysing mtDNA sequence data.

At best, one uses a diversity index which is insensitive to sample size 
off course, but nevertheless, it would be nice to be able to define a 
measure for haplotype diversity, No of polymorphic sites, etc. when you 
have a dataset with unequal sample sizes among the populations/groups.

Below, I post the answers I received thus far. If you are developing a 
package that can handle this problem, please keep us informed.

Thanks to everybody,
Dieter Anseeuw.

Dieter,
The HP-Rare software might be useful for performing rarefaction on haplotypes diversity. The program uses the Genepop format for input files, but you could code the genotypes as having a missing allele. 

Steven Kalinowksi

Hello Dieter.
I am working on such a program, but it will not be ready until the new 
year.  I am unaware of any programs that can do these calculations.  If 
you receive some responses referring to existing programs I'd like to 
know, as I will be able to save myself a lot of time.

Joseph W. Brown

Hey Dieter, a common procedure we use to correct for non sampling
errors is solving the Cornuet and Aries algorithm:
- Cornuet JM, Aries F (1980) Number of sex alleles in a sample of
honeybee colonies. Apidologie, 11: 87-93.

Rodolfo Jaffé R.

-- 
Dieter Anseeuw
Katholieke Universiteit Leuven Campus Kortrijk
Subfaculteit Wetenschappen
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Belgium

Direct phone: +32.(0)56.24.61.72
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