Software for Mcdonald-Kreitman test

Question

[zhangtao]

Hi all,

It's my first time to ask question here~~

In brief, I want to do McDonald Kreitman test for all the protein coding genes in a species' genome.

Now I have a ref genome of a species, and a .gff file for gene annotation which can tell me where gene and it's CDS is.

Also, I have a .vcf file that contain several samples of this species(e.g. human) and several samples of a closely related species(e.g. chimp).

So, is there any software to do MKT using just the ref genome and gff, vcf files.

many thanks.

[407832543]

I want to ask if you have solved your needs? If it is solved, I would like to ask, how to solve it? Because my data also needs to be calculated MKT.

Answer 1

[Jean-Karim Heriche]

There's a website for MKT and the test is also available in the PoPGenome R package.

[zhangtao]

Thank you.

I have noticed this website , package PopGenome and software DNAsp.

But as I know, website for MKT and DNAsp can only do MKT for a single or a few genes.

So, can PopGenome manage many genes(e.g. 20000 genes) in one single R script?

[Jean-Karim Heriche]

You could parallelize the task.

[zhangtao]

Yeah~ I'm trying to do like this.

thank you so much ~