The Needleman-Wunsch algorithm is a member of the class of algorithms that can calculate the best score and alignment of two sequences in the order of mn steps, where n and m are the sequence lengths. The substitution matrix and gap opening and extension penalties are user-specified. Needleall finds the alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix, minus penalties arising from opening and extending gaps in the aligned sequences. A scoring matrix is read that contains values for every possible residue or nucleotide match.

The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. Needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. Many-to-many pairwise alignments of two sequence sets Please help by correcting and extending the Wiki pages. The master copies of EMBOSS documentation are available

Needleman wunsch algorithm python