In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain. 
MAFFT
In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain.  Subsequently, mutation points as SNPs are identified by Nextstrain. 
Nextstrain
Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. 
PolyPhen-2
Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. 
I-Mutant 2.0