**4.3. Methods to compute linkage disequilibrium**

Linkage equilibrium refers to the statistical independence of alleles at all loci and indicates evidence of free recombination [83]. Thus, linkage disequilibrium is a measure of the correla‐ tion between the occurrences of nucleotides at different loci of the genome. The extent to which recombination occurs can be estimated in terms of the degree of linkage disequilibrium [84] using measures made available by specialized programs such as Linkage Analysis (LIAN) [83] and DNA Sequence Polymorphism (DnaSP) [85]. The extent of linkage can be inferred based on the following parameters.


#### **Case studies:**

LD provides a good measure for analysing the extent of recombination in viruses [82, 87]. For example, in case of *Rhinoviruses,* low values for LD measures (IS A = 0.0666, *p* < 10−4; |*D*'| = 0.5409 and that of *r2* = 0.0613) were observed and correlated well with the evidence of recom‐ bination obtained using independent methods [82]. Similarly, LD analyses in serotypes of *Foot and mouth disease virus* [87] helped to reveal low values of |*D*'| and *r2* , supporting high recombination.
