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.
Gene Finding CodonPreference finds possible protein coding regions. Third position bias in the codon can also be displayed. TestCode plots a measure of the non-randomness of the composition at every third base. TestCode uses the statistical method of Fickett based on the period three compositional constraints in the entire nucleic acid database to identify and display protein coding regions. Frames displays open reading frames for the six DNA translation frames.