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