Dear Evoldir members, 
a few days ago I have posted a question: 

"Dear EvolDir members, 
I have a dataset consisting in COI sequences from several catshark
populations with different sample size (7 < N < 24). In order to obtain
comparable estimates of genetic diversity, I would like to employ
a rarefaction algorithm. Can anyone suggest me a rarefaction method
similar to those employed with microsatellites and if there is any
software performing such analysis on mtDNA data? "

I would like to thank all the people who have answered me: you are great!!
I have decided to use CONTRIB v. 1.02, theory is described in Petit et
al., 1998.

Best regards, Michele Barbieri 

here are the answers I have received: 

#1 
You can do it easily in R. 

You just need to put your alignment into a DNAbin object. You can then
use the following script to do, one population at a time. It would be
easy to then implement something like the following script. I'll leave
the transforming the sequence data into a DNAbin object as homework.

Good luck... 

Anders. 

#2 
Hello, 

I use HP-RARE by Kalinowski: 
http://www.montana.edu/kalinowski/Software/HPRare.htm 

I hope that helps, 

Violeta 

#3 
Hi Michele, 

You could consider haplotypes as species, and use EstimateS to do your
rarefaction.

Cheers, eric 

#4 
Collaps your sequences into haplotypes and use the rarefaction calculator at 
http://www.biology.ualberta.ca/jbrzusto/rarefact.php#Inputs 
Best, 
Patrick 

#5 
Hi Michele, 
I have used the software RAREFAC developed by Petit et al. Attached is
the 'manual' with instructions on where to download it.

Good luck! 
Mariana 

#6 
Dear Dr Barbieri, 

I don't know if it could help you but I recently developed a toolbox 
(SPADS 1.0, for "spatial and population analysis of DNA sequences") to 
perform several analysis on DNA sequence datasets. Among these analyses, 
there is the computation of the allelic richness (El Mousadik & Petit 
1996). 

The program note presenting this software is currently submitted to 
Molecular Ecology Resources but the software itself is fully available 
(along with a detailed manual) at this address: 
http://ebe.ulb.ac.be/ebe/SPADS.html 

Like I said, I don't know if this is exactly what you are looking for, 
but do not hesitate if you have any question regarding the use of SPADS. 

Best wishes, 

Simon 

#7 
Dear Michele 

This paper introduced a method 
Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for
conservation on the basis of genetic markers. Conservation Biology,
12, 844-855.

that is implemented with the application "Contrib" 

I don't recall all the details right now but I've used it in the past,
eg doi: 10.11186/1741-7007-8-60

good luck, 

Kathryn 

#8 
A long time ago we used a rarefaction method to study coyote mtDNA
genotype diversity, and this was published in Genetics in 1991,
attached. It may be useful to your study.

Best wishes, Niles 

OTHER ANSWERS FROM ResearchGate: 

#9 
You could try the rarefraction program by Steven Hollond, available from:
http://www.uga.edu/strata/software/ This software has been used for COI
data before e.g.: Aguilar, Aquatic Sciences (2011) 73:153-20 Martin

#10 
Our colleague Yi Zhang from Beijjing uses the Adze program for mtDNA
allelic richness and said it was very easy Johannes

#11 
Also see Rarefac at
http://www.pierroton.inra.fr/genetics/labo/Software/Rarefac/. It is
designed specifically for use with mtDNA datasets but also can accommodate
diploid ones (e.g., msats)

Evan 
-- 

Michele Barbieri Ph.D. 
Università di Pisa 
Dipartimento di Biologia 
Unità di Biologia Marina ed Ecologia 
Via Derna 1, 56126, Pisa - Italy (I) 
Tel: +39 050 2211447 
Lab: +39 050 2211407 
Fax: +39 050 2211410 

mbarbieri@biologia.unipi.it