Multiple Sequence Analysis

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Version 8.1-UNIX

Printed: April 22, 1996 15:51

The first four programs in this section allow you to display multiple sequence alignments. The last three programs are modified verions of the GCG profile programs, supporting automatic translation of nucleotide sequence database entries, and modifications to allow searches of far larger databases.

PrettyPlot (+)

PrettyPlot displays multiple sequence alignments and calculates a consensus sequence. It does not create the alignment, it simply displays it.

PrettyBox (+)

PrettyBox displays multiple sequence alignments as shaded boxes in Postscript format (e.g., the output file must be printed and/or displayed on a Postscript-compatible device). PrettyBox will optionally calculate a consensus sequence. The program does not create the alignment; it simply displays it.

PlotAlign (+)

PlotAlign takes a GCG format sequence alignment, and plots the mean and range of values for any amino acid parameter you supply. The "panel file" contains a list of parameters to be plotted. The main database of parameters is taken from Nakai et al. (1988), and the default panel file uses selected parameters from the 13 discrete clusters in that paper. This program is experimental. Any suggestions would be most welcome.

PepAllWindow (+)

PepAllWindow plots measures of protein hydrophobicity according to the method of Kyte and Doolittle.

EPlotSimilarity (+)

EPlotSimilarity plots the running average of the similarity among the sequences in a multiple sequence alignment.

PolyDot (+)

PolyDot compares two sets of sequences, draws a dotplot for each pair of sequences, and reports all identical matches of a specified length.


TProfileSearch uses a profile (representing a group of aligned protein sequences) as a probe to search the nucleotide database for new sequences with possible protein products having some similarity to the group. The profile is created with the program ProfileMake.


TProfileSegments makes optimal alignments showing the segments of similarity found by TProfileSearch.


TProfileGap makes an optimal alignment between a profile and a sequence.

ProfilePlot (+)

ProfilePlot produces a graphical report of the frequency of patterns in a protein or nucleotide sequence.


SortConsensus identifies the strong consensus regions of an alignment in an MSF file and reports them in sorted order.


ELineUp is a screen editor for editing multiple sequence alignments. You can edit up to 500 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.


MultAlign does a simultaneous alignment for two or more DNA or protein sequences. It introduces a certain number of gaps into either pairwise aligned sequences or groups of sequences to find a minimal global distance. The user can influence the result by defining the order in which the sequences will be aligned. The program is based on a generalization of the algorithm of Waterman, Smith and Beyer by Krueger and Osterburg.


EClustAlW calculates a multiple alignment of nucleic acid or protein sequences according to the method of Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994). This is part of the original ClustalW distribution, modified for inclusion in EGCG.

ClusTree * (+)

ClusTree computes a phylogenetic tree according to the Neighbor-Joining Method of Saitou and Nei (1987). This is part of the original ClustalW distribution, modified for inclusion in EGCG. The tree will be displayed graphically.

ProfAlign *

ProfAlign is for taking two old aligments (or single sequences) and aligning them with each other. The result is one bigger aligment. This is part of the original ClustalW distribution, modified for inclusion in EGCG.