The final multiple alignment is sent to a file whose name is profalign.aln. The output is self explanatory. Any or all of the sequences in this file can be used by any other GCG or EGCG sequence analysis program. BoxAlign does not compute an alignment, it simply displays it. The tree will be displayed graphically.
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. MultAlign does a simultaneous alignment for two or more DNA or protein sequences.