An approximate phylogenetic order of the sequences is first determinded by a series of pairwise alignments using the Needleman and Wunsch method. Any subclusters that may exist in the set are prealigned before the final alignment is undertaken. Finally, the phylogenetic tree of the sequences is plotted in the form of a dendrogram. PileUp creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment.
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. Motifs can display an abstract of the current literature on each of the motifs it finds. ProfileGap makes an optimal alignment between a profile and a sequence.