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.