Fst calculation programs

[bluejay]

Hi,

 

I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics?

 

 

Thanks!

[MedGen]

Hi,

 

I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics?

 

 

Thanks!

 

Arlequin is a population genetics program that takes several different sequence types, including whole sequence, SNPs, microsatellites, etc. It's quite computationally heavy if you've got a lot of samples or a lot of variants. It doesn't use R, but rather a much friendlier Java-based front end. Might be worth checking out:

http://cmpg.unibe.ch/software/arlequin3/

 

I've used this in the past for crunching through large amounts of variation data for a number of populations and found it to be reliable. The only down side is the formatting is very fickle, every single line in the project file has to be absolutely correct, which can be a bit of a pain when dealing with large numbers of samples, and/or variants. I found setting it up in Excel first helped then C&Ping to text pad format.

 

It does allow you to calculate Fst, but only as population differentiation for a set of variants, but not for each variant individually, so it may not be exactly what you're after.