category: Sequence - Pairwise Similarity

programs:

• align - Pairwise global sequence alignment
• d3hom - Dot-matrix DNA similarity, k=3
• d4hom - Dot-matrix DNA similarity, k=4
• dotter - Dotmatrix comparison for DNA and Protein sequences
• fasta - Sequence database similarity
• ggsearch - global alignment of two DNA or protein sequences
• glsearch - global alignment of DNA or protein query sequence with local alignments of database sequences
• lalign - Rigorous local pairwise alignment
• last-dotplot - Create a dotplot from a last alignment
• last-map-probs - Calculate a mismap probability for each alignment.
• p1hom - Dot-matrix protein similarity, k=1
• p2hom - Dot-matrix protein similarity, k=2
• relate - Statistical significance of database similarity
• tfastx - compare a protein to a DNA database, calculating similarities with frameshifts
• tfasty - compare a protein to a DNA database, calculating similarities with frameshifts