a suite of programs for sequence alignment including: aln, swg, prrn, phyln and makmdm.
aln: Pairwise alignment of biological sequences supporting spliced alignment procedures.
swg: locally aligns a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow.
prrn: global multiple alignment of a set of protein or DNA sequences by doubly nested iterative refinement method.
phyln: UPGMA or NJ method to make a phylogenetic tree from a multiple alignment.
makmdm: constructs binary PAM matrices. Must be run once before the first run of aln, swg or prrn.