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.
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zhangtao •
There's a website for MKT and the test is also available in the PoPGenome R package.
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?
You could parallelize the task.
Yeah~ I'm trying to do like this.
thank you so much ~
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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.