How to interpret a pairwise distance matrices for X nr-SNPs sliding windows across the genome

Question

[serpalma.v]

Hi everyone,

I am new at bioinformatic concepts such as sliding window algorithm. I am currently reading a paper where this concepts appears. And states:

We generated 13-by-13 pairwise distance matrices for 25-SNP sliding windows across the genome.

This is shown in figure 1D in Chan et al 2012.

http://linkinghub.elsevier.com/retrieve/pii/S0960982212002680

My questions are:

• Can this be minimized to a simpler expression for the non-bioinformatic?
• How to interpret the pair-wise distance matrix?
• What background should I learn to understand this?

Thanks