VSNS BioComputing Division Multiple Alignment Resource Page

Calculation of Multiple Alignments on the WWW :

Services offering several methods

(NEW August 19, 2006) http://msa.cgb.ki.se
A website to compute (Kalign), visualize (Kalignvu) and evaluate (MUMSA) multiple sequence alignments.

(NEW March 7, 2005) http://www.charite.de/bioinf/strap/
STRAP: Interactive program for generating and analyzing multiple sequence alignments. Multiple structure alignments, integrated 3D-viewer, 3D-superposition of protein backbones, mapping of mutations onto 3D-models, translation of nucleotide sequences to amino acid sequences, sequence dotplots.

(NEW May 9, 2001) http://cbcsrv.watson.ibm.com/Tmsa.html
MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences, and related tools

http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html
Baylor's search launcher for Biologists, Multiple Alignment section
ClustalW, MAP, PIMA 1.4, MSA 2.1, and BLOCK MAKER alignments
(There are also ClustalX, and ClustalW alignments in color)

(NEW Oct 7, 1997) http://www.ibcp.fr/both.html
Clustalw + Multalin Multiple Alignment at IBCP

http://cbrg.inf.ethz.ch/MultAlign.html
Calculate, optimize and score multiple sequence alignments with ProbModel,
MSA, ClustalW and heuristics. The scoring is a probabilistic measure.

Services offering a method that seems to be generally applicable

(NEW July 20, 2005) http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/
JEvTrace - algorithms and multivalent graphical browser for combined alignment, phylogeny, and structure analysis.

(NEW Mar 11, 2003) http://baboon.math.berkeley.edu/mavid/
MAVID - multiple alignment program for large genomic regions

(Updated Nov 2007) http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ (new server)
http://align.bmr.kyushu-u.ac.jp/mafft/software/ (download site)
MAFFT - Fast Multiple Alignment Program for Amino Acid or Nucleotide Sequences

(NEW Feb 6, 2003) http://www.ch.embnet.org/software/TCoffee.html
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model.

(NEW Mar 19, 1998) http://godzilla.dcrt.nih.gov/~yap/museqal2.html
MUSEQAL optimal multiple alignment by iteratively improving a given set of pre-aligned sequences.

http://bibiserv.techfak.uni-bielefeld.de/dca/
DCA: Divide and Conquer Multiple Sequence Alignment
Close-to-optimal, fast simultaneous sum-of-pairs alignment of up to
twenty protein, DNA, or RNA sequences

http://bibiserv.techfak.uni-bielefeld.de/dialign/
DIALIGN - fragment-based alignment program following the method described
by Morgenstern et al. in PNAS 93 (22), pp. 12098-12103.

http://cartan.gmd.de/ToPLign.html
ToPLign: Toolbox for Protein Alignment
Computing, analysis and visualization of pairwise, multiple, threading,
and parametric alignments.

http://www.ibc.wustl.edu/msa.html
MSA, (Close-to-) Optimal Alignments using the Carrillo-Lipman bound

http://www.toulouse.inra.fr/multalin.html
Computing and visualization of multiple alignments with MultAlin
(Corpet's method, similar to Clustal)

http://cbrg.inf.ethz.ch/subsection3_1_1.html
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.

(New Feb 9, 1998) http://genome.cs.mtu.edu/map.html
MAP - computes a multiple global alignment using iterative pairwise method.

Services offering a method that seems to be applicable to Proteins

(NEW Mar 19, 1998) http://bmerc-www.bu.edu/protein-seq/pimaII-new.html
Protein sequence analysis and multiple alignment with pimaII

(NEW Mar 19, 1998) http://bonsai.lif.icnet.uk/bmm/dsc/dsc_form_align.html
DSC: Discrimination of Protein Secondary Structure Class via making a multiple alignment

(NEW Mar 19, 1998) http://croma.ebi.ac.uk/dali/
Dali server is a network service for comparing protein structures in 3D
You submit the coordinates ... multiple alignment of structural neighbours is mailed back

(New Feb 9, 1998) http://www-bio.lirmm.fr:8090/map123d.html
Global multiple alignment module that allows the alignment of protein
primary structures as well as tertiary structures.

(NEW Oct 7, 1997) http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html
MATCH-BOX - simultaneous alignment of several protein sequences
where each sequence position is weighted by a reliability score

http://www.icnet.uk/bmm/dsc/dsc_form_align.html
DSC: Protein sequence alignment and secondary structure prediction.
Alignment by heuristic combination of Blastp, Smith-Waterman, and Clustalw.

http://www.embl-heidelberg.de/predictprotein/predictprotein.html
MaxHom Alignments (offered together w/ structure prediction)
Info: http://www.embl-heidelberg.de/predictprotein/phd_help.html#P3PIR

http://www.cse.ucsc.edu/research/compbio/sam.html
SAM: Sequence Alignment and Modeling.
Hidden Markov model multiple alignment and discrimination.

http://www.genebee.msu.su/services/malign_reduced.html
GeneBee Multiple alignment: pairwise motifs -> multiple motifs -> "supermotifs"
-> construction of multiple alignment.

http://www-biol.univ-mrs.fr/english/logligne.html#align
Long list of alignment/phylogeny WWW services. (see also Inge Jonassen's list).

Analysis of Multiple Alignments :

(Added Dec 30, 1998) http://www.bork.embl-heidelberg.de/Alignment/
Pasting positions to the left and/or right of a CLUSTAL alignment, inter-block gap sizes and mismatches between aligned sequences and master sequences, consensus calculation

(Added Dec 30, 1998) http://www.sdsc.edu/MEME/meme/website/
Discover motifs (highly conserved regions) in groups of related DNA or protein sequences

(Added Feb 9, 1998) http://www.blocks.fhcrc.org/process_blocks.html
Blocks are carved out from protein multiple sequence alignments for logos,
trees and other displays, and for blocks-based searches.

http://barton.ebi.ac.uk/servers/amas_server.html
AMAS - Analyse Multiply Aligned Sequences
Visualization of physico-chemical properties of the columns of an alignment

http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi
WebLogo Sequence Logo Generation Main Form
Visualization of the conservation (and more!) of the columns of an alignment

(NEW Sep 22, 1997) http://www.lctn.u-nancy.fr/viseur/services.html
Viseur's WWW service: converts alignments in MSF format to
text-based, graphical and style-sheet HTML representations.

http://ulrec3.unil.ch/software/BOX_form.html
BOXSHADE, Pretty Printing and Shading of Multiple-Alignment files.

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.)

(Added Feb 9, 1998) ftp://ftp.genome.ad.jp/pub/genome/saitama-cc/
Multiple alignment by randomized iterative strategy (Gotoh's RIW/DNR methods).

(Added Feb 9, 1998) http://www.vims.edu/~mes/hennig/software.html#malign (alternative link)
Malign - parsimony-based alignment program for molecular sequences.

(Added Feb 9, 1998) ftp://ftp.bio.indiana.edu/molbio/align/macaw/
MACAW - for locating, analyzing, and editing blocks of localized
sequence similarity and linking them into a composite alignment.

(Added Feb 9, 1998) ftp://ftp.ebi.ac.uk/pub/software/unix/treealign.tar.Z
Treealign - Multiple sequence alignment and phylogeny,
cf. J. Hein, Meth. Enzymol. 183 (1990), 626-644. (Info on VMS-version)

(Added Feb 9, 1998) http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/UnivAln/UnivAln.pm.html
Bio::Aln - Perl object for reading, parsing, slicing, and manipulating alignments.

http://www.cs.monash.edu.au/~lloyd/tildeStrings/index.html
(1) Iterated, stochastic 3-way alignment at each internal node of the evolutionary
tree to sample ancestral strings, and (2) a fast 3-way alignment procedure.

http://genome.wustl.edu/eddy/hmmer.html
HMMER -- Hidden Markov model software "to do multiple sequence alignment and
very sensitive database searching".

ftp://juno.ucsd.edu/progs
Programs for progressive alignment (Feng & Doolittle) of protein sequences
and the construction of phylogenetic trees from them. (See file readme.doc)

http://www.genetik.uni-koeln.de/dnaplot/dnaplot.html
DNAPLOT: an alignment tool for immunologists
See also the DNAPLOT Search Page

http://www.icot.or.jp/ICOT/IFS/IFS-abst/ifs-catalogue.html
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.

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2/
CINEMA - Colour INteractive Editor for Multiple Alignments
Java-Tool for the visualisation and manipulation of both protein and DNA sequences

http://indigo2.uia.ac.be:80/~peter/dcse/
DCSE (Dedicated Comparative Sequence Editor)

ftp://morgan.angis.su.oz.au/pub/unix
ShadyBox is a drawing program which enables you to box and shade regular
and irregular shaped segments of aligned multiple sequences.

(NEW Sep 22, 1997) http://www.lctn.u-nancy.fr/viseur/viseur.html
Viseur: transmembrane proteins/GPCRs visualization, protein MSA editor/viewer
with per residue annotation, HTML generation, etc.. (for SGI workstations)

http://www.ebi.ac.uk/biocat/biocat_algt.html
BioCatalog, Section on (Multiple) Alignment search software, editing
and display, and browsers.

Databases:

http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/databanks.html
1996 Collection of Databanks relevant to Multiple Alignment
3d-Ali, ALIGN/PRINTS, FSSP, HSSP, PIRALN, GCRDb/TM7, HHS

Tutorial texts:

(NEW June 16, 1999) http://bioinformatics.weizmann.ac.il/~pietro/Making_and_using_protein_MA
Introduction to making and using protein multiple alignments, by Shmuel Pietrokovski

http://geoff.biop.ox.ac.uk/papers/rev93_1/rev93_1.html
Protein Sequence Alignment and Database Scanning, by Geoffrey Barton
ca. 30 pages text, 10 figures.

http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/mulali.html
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.

http://www2.pasteur.fr/~tekaia/MAcours/multalign.html
Multiple Sequence Alignments, by Fredj Tekaia, under construcution
ca. 5 pages text

http://www2.pasteur.fr/~tekaia/MAcours/clustalw.html
ClustalW tutorial, by Fredj Tekaia.
ca. 5 pages text

http://biotech.bio.tcd.ie/acerhelp/ClustalW-Acerhelp.RTF.txt.html
ClustalW tutorial, Andrew T. Lloyd
ca. 5 pages text

http://lenti.med.umn.edu/MolBio_man/MolBio_man.html
AGRENET's Unofficial Guide to GCG Software
ca. 50 pages text

http://www.dl.ac.uk/embnet.news/vol2_1/align.html
A short introduction to algorithms for multiple sequence alignments
ca. 4 pages text

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