First, percent divergence figures are calculated between all pairs of sequences. These divergence figures are then used by the NJ method to give the tree. A New Method for Reconstructing Phylogenetic Trees. This is the plot from the example session. BoxAlign does not compute an alignment, it simply displays it.
LineUp is a screen editor for editing multiple sequence alignments.
You can edit up to 30 sequences simultaneously. New sequences can be typed in by hand or added from existing sequence files. A consensus sequence identifies places where the sequences are in conflict. MultAlign does a simultaneous alignment for two or more DNA or protein sequences. It introduces a certain number of gaps into either pairwise aligned sequences or groups of sequences to find a minimal global distance.