I am asking another ka/ks related question! I am a bit of a beginner with this stuff so go easy.
I understand the the Ka/ks ratio is used mainly for interspecies comparisons..is a way of assessing what type of selection is acting on a gene.
I know it is also usable for intraspecies comparisons...so different coding sequences of the same gene can be compared to assess what selection is acting on the gene - this is what I would like to do - I have the CDS sequence for >2000 individuals that I have sequenced. Most of them do not have any changes to the coding sequence..as this gene is likely to be essential - no premature stop codons etc have been found.
I plan to do the analysis using DNAsp....do I input the CDS sequence for ALL individuals? Or do I input JUST the 200 or so variable ones and the original CDS sequence..?
Secondly, as you get a ka/ks for each individual sequence...do I average this to assess what's going on overall?
I am pulling my hair out...I have a deadline, I am so confused - any help would be SO appreciated!