#Why MSA is necessary?
A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally a protein, DNA, or RNA. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences shared evolutionary origins.
#What challenges are to be faced by using MSA?
Accuracy has been a traditional limitation of multiple sequence alignments for the last 20 years, and it is no surprise that this issue has been the most actively addressed, if only because inaccurate alignments are simply useless. The other interesting development has been the increase in the number of sequences. Traditionally, the length of the sequences (L) was greater than the number of sequences (N), and most methods were tuned so that they could deal with any value of L, assuming N would not be a problem. This is especially true of consistency-based methods that are cubic in complexity with N, but only quadratic with L. With N << L, the extra cost incurred by consistency remains manageable, but things degrade rapidly when N becomes big.
Applying DP is also difficult in such cases, we might have to choose a greedy approach instead of DP there.