Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman. Figure makes figures and posters by drawing graphics and text together. You can include output from other GCG graphics programs as part of a figure. 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. PlotSimilarity plots the running average of the similarity among the sequences in a multiple sequence alignment. The GapShow display stops when the shorter sequence is exhausted.