Multiple Alignment Resources on the WWW

Georg Fuellen fuellen at
Wed Nov 1 16:28:59 EST 1995

The following is the Multiple Alignment Resource Page
developed for the GNA-VSNS Biocomputing Course, see

This list, and any updates are available at:

Email them to fuellen at
Also, please mail me corrections, updates, flames, etc !

Analysis of Multiple Alignments :
AMAS - Analyse Multiply Aligned Sequences 
Visualization of physico-chemical properties of the columns of an alignment
WebLogo Sequence Logo Generation Main Form
Visualization of the conservation (and more!) of the columns of an alignment

Calculation of Multiple Alignments on the WWW :

(Most Fill-Out Forms include a link to the software itself, e.g.
ClustalW, MSA, and ToPLign)
Baylor's search launcher for Biologists, Multiple Alignment section
ClustalW, PIMA, MAP, and BLOCK MAKER alignments
Baylor/UH search launcher for Biologists, Multiple Alignment section
ClustalW, PIMA, MAP, BLOCK MAKER and TreeAlign alignments
ToPLign: Toolbox for Protein Alignment
Computing, analysis and visualization of pairwise, multiple, threading, 
and parametric alignments.
MSA, (Close-to-) Optimal Alignments using the Carrillo-Lipman bound
CLUSTALW, Heuristic Multiple Alignments using Alignment Along a Tree
AllAll: Calculate Phylogenetic Trees, Alignments, dSplits, Probabilistic 
ancestral sequence, {Kabat-Wu, probability, maximum likelihood} variation index,
prediction of Surface/Interior/Active site, prediction of parse regions.
MaxHom Alignments (offered together w/ structure prediction)
MRA, Alignment for Many Sequences by Comparison of Dot-matrices.
GeneBee Multiple alignment: pairwise motifs -> multiple motifs -> "supermotifs" 
-> construction of multiple alignment. 

Collection of Databanks relevant to Multiple Alignment

Tutorial texts:
Protein Sequence Alignment and Database Scanning, by Geoffrey Barton
ca. 30 pages text, 10 figures.
A Gentle Guide to Multiple Alignment, by Georg Fuellen
ca. 50 pages text, ca. 20 figures, exercises, solution sheet.
A lot of the resources mentioned here are treated in detail in part 3.3,
e.g. MSA/Clustal and, by way of exercises, AMAS and WebLogo.
Multiple Sequence Alignments, by Fredj Tekaia, under construcution
ca. 5 pages text
ClustalW tutorial, by Fredj Tekaia.
ca. 5 pages text
ClustalW tutorial, Andrew T. Lloyd
ca. 5 pages text
AGRENET's Unofficial Guide to GCG Software
ca. 50 pages text

Software packages:

(Some software packages offer a Fill-Out Form for doing calculations 
by way of a WWW server; they are listed above, e.g. Clustal, MSA, and ToPLign.)
BioCatalog, Section on (Multiple) Alignment search software, editing 
and display, and browsers.
Various software packages (No. 55,56,75,76,93-95) running on parallel computers
Dynamic Programming, Simulated Annealing, Genetic Algorithm, Iterative 
Improvement, Intelligent Refinement, RNA-Sequence Considering Stem Regions.

Starter page for various software packages 
MEGA, GDE, Phylip, etc
SAM: Sequence Alignment and Modeling System
DCSE (Dedicated Comparative Sequence Editor)
ShadyBox is a drawing program which enables you to box and shade regular
and irregular shaped segments of aligned multiple sequences.

(Thanks to the Molecular Biology Computational Resource at Baylor College Of 
Medicine, and the Manchester and North High Performance Computing Training 
and Education Centre (MAN T&EC) for mirroring assistance.)

best wishes,
fuellen at dali.Mathematik.Uni-Bielefeld.DE, fuellen at MIT.EDU

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