batukargili / bionformatics-globalalignment

Java code that finds pairwise sequence alignments for all possible pairs of sequences and construct similarity matrix.

bionformatics-globalAlignment

Java code that finds pairwise sequence alignments for all possible pairs of sequences and construct similarity matrix.

• Finds pairwise sequence alignments for all possible pairs of sequences.

• Global alignment to find each pairwise sequence alignment constructed

• Match and mismatch scores for amino acids are taken from the BLOSUM62 matrix.

• Similarity Score (s i , s j ) = # of exact matches / aligned sequence length

• Constructs similarity matrix (kxk) by using similarity scores.

• Builds guide tree with using similarity matrix.