OldDistances makes a table of the pairwise similarities within a group of aligned sequences. OldDistances writes a matrix of the pairwise similarities between up to 50 different sequences in a multiple sequence alignment. Matches A match occurs if the value in the scoring matrix for a pair of bases or amino acids is greater than or equal to a set match threshold. It can also plot a tree showing the clustering relationships used to create the alignment.
Gap makes sequence alignments.
LineUp edits multiple sequence alignments. ProfileGap aligns a new sequence to an existing multiple sequence alignment. Pretty displays multiple sequence alignments. Distances writes a matrix of the pairwise genetic distances between sequences in a multiple sequence alignment. These distances are suitable for input into programs such as GrowTree that create evolutionary trees.