Table 1.

Comparison of the alignment-based and alignment-free algorithm (present study).

	Alignment based method	Alignment free method (Present Study)
Processing time	It needs vast CPU time which is proportional to NK. K is the number of sequences for alignment and N is the length of each sequence	It is based on successive two-dimensional dynamic programme for nucleotide density determination. It takes less CPU time which is proportional to N2
Handling in divergent sequence	Alignment-based approach works well for closely related sequences. In case of divergent sequences, a reliable alignment is difficult to be obtained	Alignment-based approach is workable for divergent sequences efficiently
Editing in sequence	This method requires editing in the sequence	This method does not require any editing in the sequence
Nature of algorithm	It requires dynamic programming, which is computationally expensive, to obtain alignment with optimal score	It relies on dynamic programmingby indexing word counts, without any optimization
Homology search	This method assumes the contiguity of homologous regions in the sequence	The assumption of homologous region contiguity is not required in alignment-free method