What Is Most Powerful Selection Signature Detection Tool Which Meanwhile Has Decent Low Fdr?

Question

[Griffan]

I was trying to identify neutral sites of several individuals' genome from a population, do you guys have any idea of what tools should be the most suitable ones?

The data is NGS, whole genome.

Answer 1

[Chrispin Chaguza]

I'm not sure which tool is the most powerful as each one performs better using its optimal criterion. I think it all depends on the particular dataset that you're working with. As pointed out by Zev.Kronenberg, several methods can be used. Check MEGA and DnaSP tools, I think they have built-in functionality for such type of analysis included. If you want to determine gene-wide selection (or neutral evolution), you could try using Ka_Ks_Calculator by Professor Ziheng Yang.

Answer 2

[JMR]

A new (very user friendly) implementation of most extended haplotype test statistics is out.

From the manual:

selscan currently implements EHH, iHS, and XP-EHH, and requires phased data.
It should be run separately for each chromosome and population (or population
pair for XP-EHH). selscan is 'dumb' with respect ancestral/derived coding and
simply expects haplotype data to be coded 0/1. Unstandardized iHS scores are
thus reported as ln(iHH1/iHH0) based on the coding you have provided.

Here's the link: https://github.com/szpiech/selscan

Answer 3

[Zev.Kronenberg]

Tajima's D, iHS, EHH, Theta or PI. Those are just a few, but it is hard to tell what you are trying to do.