My question is general not for a specific data. I could not find any information in the literature or I somehow missed it. So, my question is that how could it be considered two or more variations at the same position for different individuals, like in polyploid organisms ? I shared a figure below to be more clear.
So let's assume It is SNPs data among the chromosome for one individual and there are many individuals in a same way. Let's consider first position, in the image only two different variation is there and one of which is found in chr 3 and other chrs.. How could it be considered all variation between chromosomes for further analysis, like, ordination analysis or cluster tree for individuals? More, If the number of variation increase, how could it be handled ? Do you guys know if there is any publication about it ?
I am not sure if it is just me but I do not understand what you are asking.
Sorry for confusion. Simply, when calculating genetic differentiation between individuals, I want to consider not just one variation in positions, but also other variations. Those kind of variations are linked to each other. I am not sure If I should directly implement the distance algorithm on them. Now is it clear ?
Unfortunately not. Are you talking about phase information being used to look at the relationship between samples/individuals? Or whether when calculating the relationship you should take into consideration all alleles at each position?
I'm talking about considering all alleles at each position when calculating relationship.