Variations around the Needleman and Wunsch Algorithm (Perl)

1 Install and run this Perl implementation of the Needleman and Wunsch algorithm [nw] in order to align these two sequences: A and B. Examine the code to figure out how the sequences should be provided to the program
Solution:./ seq1.fasta seq2.fasta
2 What is the cost for a substitution? an Indel?. Modify the scoring scheme so that the program produces this alignment:
Solution: [nw_2]
3 Modify the code so that it prints out the score of the alignment
Solution: [nw_3]
4 Modify the recursion so that INDELS get different penalties in sequence A and B
Solution: [nw_4]
5 Modify the recursion so that the alignment becomes local (Smith and Waterman)
Solution: [sw]