Pairwise Comparison DotPlot graphically displays the alignment between two sequences. Multiple Sequence Analysis PileUp creates a multiple sequence alignment for up to 500 sequences. PileUp creates a multiple sequence alignment of up to 500 sequences using the method of Feng and Doolittle, similar to the method of Higgins and Sharp. A dendrogram illustrating sequence similarity is also created using the strategy of Sneath and Sokal. PileUp can also create a dendogram to graphically show sequence similarity.
LineUp is an interactive editor for editing multiple sequence alignments.
Pretty displays multiple sequence alignments. You can search a database of sequences with these profiles using the MotifSearch program. NoOverlap identifies the places where a group of nucleotide sequences do not share any common subsequences. GrowTree creates a phylogenetic tree for a group of aligned sequences. Distances writes a matrix of the pairwise evolutionary distances between aligned sequences.