red_bullet.gif (914 bytes) ALIGN  Query using  sequence data (GENESTREAM SEARCH network server IGH Montpellier, France) - Very nice output.
red_bullet.gif (914 bytes) LALIGN - (EMBnet) finds multiple matching subsegments in two sequences.  Provides one with % identity for different  subsegments of the sequence.

red_bullet.gif (914 bytes) FFAS - The Fold and Function Assignment System. The profile of a user's protein can now be compared with ~20 additional profile databases. The user can, through a series of tabs, navigate multiple results pages, and also includes novel functionality, such as a dotplot graph viewer, modeling tools, an improved 3D alignment viewer and links to the database of structural similarities. (Reference: Jaroszewski, L. et al. 2011. Nucleic Acids Res. 39(Web Server issue):W38-44)

red_bullet.gif (914 bytes) Compare Two Sequences with FASTA (W.R. Pearson, University of Virginia, U.S.A.) - offers a large number of score  matrices. LALIGN/PLALIGN - Local Alignments - offers the user a graphic "dotplot" output of the alignments.

red_bullet.gif (914 bytes) GeneWise (EMBL-EBI) - compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

red_bullet.gif (914 bytes) SIM  - Alignment tool for protein (ExPASy, Switzerland) gives fragmented alignments similar to LALIGN. 

red_bullet.gif (914 bytes) Secondary Structure Element Alignment (SSEA ) - computes alignments of protein secondary structures.  The server supports both performing pairwise alignments and searching a secondary structure against a library of  domain folds. It can calculate global and local secondary structure element alignments. (Reference: P. Fontana et  al. (2005) Bioinformatics 21: 393-395).

Protein Sequence similarity and identity scores:

 ToPLign (BioSolveIT GmbH, Germany) - requires user login. Provides a wide variety of  output formats for pairwise  alignments. 
  BLAST2 (NCBI) - also useful for DNA sequence comparisons.  Provides small graphic which is only of use with proteins or short DNA sequences.
  SUPERMATCHER (L'Institut Pasteur, France) - is part of the EMBOSS group of programs.  Use 10 and 0.5 as  the defaults in the Gap opening penalty and Gap extension penalty, respectively.
  MATCHER - f inds the best local alignments between two sequences (EMBOSS) 

red_bullet.gif (914 bytes) zPicture (Comparative Genomics , Lawrence Livermore National Laboratory, U.S.A.) - is a DNA or genome alignment and  visualization tool based on blastz alignment program. Alignments can be automatically submitted to rVista 2.0 to identify  evolutionary conserved transcription factor binding sites. 

red_bullet.gif (914 bytes) FOLDALIGN - folds and aligns RNA structures (make a foldalignment) based on a lightweight energy model and  sequence similarity. The current version makes pairwise foldalignments. (Reference: J. H. Havgaard et al. 2005.  Bioinformatics 21: 1815 - 1824).


BACKGROUND INFORMATION: There are two good on-line help sites for CLUSTAL W. These are (a) On-line help for  CLUSTAL (Wiki.) and, (b) Multiple sequence alignment, (Wiki)

Several good sites:

red_bullet.gif (914 bytes) ClustalW - Multiple Sequence Alignment (EBI, United Kingdom). This provides one with a number of options for data  presentation, homology matrices [BLOSUM (Henikoff), PAM (Dayhoff) or GONNET, and presentation of phylogenetic  trees (Neighbor-Joining, Phylip or Distance).  Sites offering ClustalW alignment are at the Pasteur Institute, Kyoto University and

red_bullet.gif (914 bytes) MAFFT Multiple sequence alignment and NJ / UPGMA phylogeny - I recently attempted to align thirteen 50kb bacteriophage genomes using ClustalW, not no success, MAFFT provided the alignment incredibly quickly. Unfortunately it would not generate a tree. The Clustal data was opened in ClustalX and the tree saved in default settings and visualized in FigTree (Reference: Katoh, K. et al. 2002. Nucl. Acids Rese. 30: 3059-3066).

red_bullet.gif (914 bytes) Clustal Omega - is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments. (Reference: Sievers, F. et al. 2011. Molecular Systems Biology 7 Article number: 539)

red_bullet.gif (914 bytes) DbClustal - (EMBL-EBI) aligns sequences from a BlastP  database search with one query sequence. The alignment algorithm is based on ClustalW2 modified to incorporate  local alignment data in the form of anchor points between pairs of sequences. Very colorful output.

red_bullet.gif (914 bytes) PROBCONS - is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN. (Reference: C.B. Do et al. 2005. Genome Res. 15: 330-340).

red_bullet.gif (914 bytes) webPRANK -  incorporates phylogeny-aware multiple sequence alignment, visualisation and post-processing in an easy-to-use web interface.
(Reference: Löytynoja, A., & Goldman, N. 2010. BMC Bioinformatics. 11:579).

red_bullet.gif (914 bytes) GUIDANCE - implements two different algorithms for evaluating confidence scores: (i) the heads-or-tails (HoT) method, which measures alignment uncertainty due
to co-optimal solutions; (ii) the GUIDANCE method, which measures the robustness of the alignment to guide-tree uncertainty. The server projects the confidence scores
onto the MSA and points to columns and sequences that are unreliably aligned. These can be automatically removed in preparation for downstream analyses. N.B. Need
at least 8 sequences(Reference: Penn, O. 2010. Nucleic Acids Res. 38(Web Server issue):W23-28).

red_bullet.gif (914 bytes) SALIGN - automatically determines the best alignment procedure based on the inputs, while allowing the user to override default parameter values. Multiple alignments
are guided by a dendrogram computed from a matrix of all pairwise alignment scores. When aligning sequences to structures, SALIGN uses structural environment
information to place gaps optimally. If two multiple sequence alignments of related proteins are input to the server, a profile-profile alignment is performed.(Reference:
Braberg, H. et al. 2012. Bioinformatics. 28(15):2072-2073).

red_bullet.gif (914 bytes)  AlignMe (for Alignment of Membrane Proteins) is a very flexible sequence alignment program that allows the use of various different measures of similarity. These
similarity measures include: substitution matrices, hydrophobicity scales and any kind of profiles (i.e. secondary structure predictions or transmembrane predictions).
(Reference: Khafizov K et al. 2014. Nucl. Acids Res. 42(W1), W246-W251)

red_bullet.gif (914 bytes) PRALINE - is a multiple sequence alignment program with many options to optimize the information for each of  the input sequences; e.g. global or local preprocessing, predicted secondary structure information and iteration  capabilities. (Reference: V.A. Simossis et al. (2005) Nucleic Acids Res. 33: 816-824). Example of  PRALINE output:

Gene Context Tool - is an incredible tool for visualizing the genome context of a gene or group of genes (synteny). In the  following diagram an RpoN (Sigma54) protein was analyzed. (Reference: R. Ciria et al. (2004) Bioinformatics 20: 2307-2308).

red_bullet.gif (914 bytes) ConSurf is is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. The degree to which an amino (or nucleic) acid position is evolutionarily conserved is strongly dependent on its structural and functional importance; rapidly evolving positions are variable while slowly evolving positions are conserved. (Reference: Ashkenazy, H. et al. 2010. Nucl. Acids Res. 38 (suppl 2): W529-W533).

red_bullet.gif (914 bytes) MultAlin - Multiple sequence alignment by Florence Corpet (Institut National de la Recherche Agronomique (INRA), France). N.B.  The results are presented in colour.

red_bullet.gif (914 bytes) Multiple Alignment - GeneBee service (Belozersky Institute of Physico-chemical Biology, Moscow State University, Russia) . N.B.  This service also provides phylogenetic analysis of the data.

red_bullet.gif (914 bytes) PROMALS - constructs multiple protein sequence alignments using information from database searches and secondary structure prediction - for protein homologs with sequence identity below 10%, aligning close to half of the amino acid residues correctly on average.   
(Reference: Pei, J. & Grishin, N.V. 2007. Bioinformatics. 23(7):802-808).

red_bullet.gif (914 bytes) DiAlign (Univ. Bielfeld, Germany) - "DIALIGN is a novel program for multiple alignment developed by Burkhard  Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties,  DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences."

red_bullet.gif (914 bytes) The Coffee Collection - T-Coffee (Aligns DNA, RNA or Proteins using the default T-Coffee), M-Coffee (Aligns
DNA, RNA or Proteins by combining the output of popular aligners), R-Coffee (Aligns RNA sequences usingpredicted secondary structures), Expresso (Aligns protein sequences using structural information), PSI-Coffee (Aligns distantly related proteins using homology extension) and TM-Coffee (Aligns transmembrane proteins using homology extension). (Reference: Di Tommaso. P. et al. 2011. Nucleic Acids Res. 39(Web Server issue: W13-17; Chang, J.M. et al. 2012. BMC Bioinformatics. 13 Suppl 4: S1).

red_bullet.gif (914 bytes)  LocARNA - Multiple Alignment of RNAs -  is a tool for multiple alignment of RNA molecules. LocARNA requires only RNA sequences as input and will simultaneously fold and align the input sequences. LocARNA outputs a multiple alignment together with a consensus structure. For the folding it makes use of a very realistic energy model for RNAs as it is by RNAfold of the Vienna RNA package (or Zuker's mfold). For the alignment it features RIBOSUM-like similarity scoring and realistic gap cost.  ( Reference: C. Smith et al. 2010. Nucl. Acids Res.  38: W373-377).

red_bullet.gif (914 bytes) CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures. Alternatively, you can also provide base pair probability matrices (dot plots in .ps format) or fixed structures (as annotation in the FASTA alignment) for your sequences. If you provide fixed structures, only those structures and not the entire ensemble of possible structures is aligned. In contrast to LocARNA, CARNA does not pick the most likely consensus structure, but computes the alignment that fits best to all likely structures simultaneously. Hence, CARNA is particularly useful when aligning RNAs like riboswitches, which have more than one stable structure. (Reference: A. Dragos et al. 2012. Nucleic Acids Reseach 40: W49-W53)

Alternative presentations of alignments:
red_bullet.gif (914 bytes) BOXSHADE: -  (Hofmann & Baron, Institute Pasteur, France) This version accepts a wide variety of file formats and allows  the requester considerable flexibility in defining the output appearance (colour and arrangement as well as format). 

red_bullet.gif (914 bytes) ESPript 3.0 - (IUniversite Lyon, France)  -  is a program which renders sequence similarities and secondary structure information from aligned sequences for analysis and publication purpose. This requires that you save your alignment as a *.aln file. Good control over output  appearance and format is available (ps, tiff and gif). (Reference:  Robert X. & Gouet P. 2014.  Nucl. Acids Res. 42 (W1), W320-W324).

red_bullet.gif (914 bytes) Multiple Align Show - ( Open Lab; University of Massachusetts Lowell) Allows considerable choice in  colouring alignments.
red_bullet.gif (914 bytes) H-BLOX (Molecular Design Laboratory, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Germany)  provides information content or the relative entropy within DNA or protein alignment blocks.

red_bullet.gif (914 bytes) MPsrch (EMBL-EBI) - this sequence sequence comparison tool  implements the true Smith and Waterman algorithm  identifying hits in cases where Blast and Fasta fail and also reports fewer false-positives. Provides information on: Match  %; % Query Match (% of the query sequence matched);  Conservative changes; Mismatches; Indels; and Gaps.

Sequence comparison between two small genomes:

red_bullet.gif (914 bytes) SCAN2 ( provides one with a colour-coded graphical alignment of genome length DNAs in Java.  In the  top panel regions of high sequence identity are presented in red. By highlighting the grey, yellow, green, black boxes one  can select specific regions for examination of the sequence alignment. For additional information on the output see here.  This site appears to work best with Internet Explorer.

red_bullet.gif (914 bytes) Advanced PipMaker - aligns two DNA sequences and returns a percent identity plot of that alignment, together with a traditional textual form of the alignment.  You might want to download Laj (Penn State -  Bioinformatics Group, U.S.A.) for viewing and manipulating the output from pairwise alignment programs such as  PipMaker representations of the alignments. (Reference: Schwartz et al. 2000. Genome Research 10: 577-586). 

red_bullet.gif (914 bytes) JDotter: A Java Dot Plot Viewer (Viral Bioinformatics Resource , University of Victoria, Canada) - a dot  matrix plotter for Java.  Produces similar diagrams to the above mentioned programs, but with better control on output.
red_bullet.gif (914 bytes) YASS - perform DNA local alignments with results in dotplot and tabular form (Reference:  L.Noe & G. Kucherov.  2005. Nucl. Acids Res. 33: W540-W543).
red_bullet.gif (914 bytes)  Dotlet - (Reference: T.Junier & M. Pagni. 2000. Bioinformatics 16:178-179)

red_bullet.gif (914 bytes) multi-zPicture: multiple sequence alignment tool (Comparative Genomics , Lawrence Livermore National  Laboratory, U.S.A.) - provides nice dotplot graphs and dynamic visualizations. If simple gene locations are provided in  the form (e.g. > 2000 5000 RNA_polymerase; indicates the the RNA polymerase gene is found on the plus strand  between bases 2000 and 5000) this data will be added to the dynamic visualization. zPicture alignments can be  automatically submitted to rVista to identify conserved transcription factor binding sites.

red_bullet.gif (914 bytes)VISTA - VISualization Tools for Alignments (Ernest Orlando Lawrence Berkeley National Laboratory, U.S.A.) - this URL allows  one to align two genome-length sequences.

GeneOrder 3.0 (D. Seto,  Bioinformatics & Computational Biology, George Mason Univ., U.S.A.)  is ideal for comparing small  GenBank genomes (up to 2 Mb). Each gene from the Query sequence is compared to all of the genes from the  Reference sequence using BLASTP. There are two display formats: graphical and tabular. Currently the graph is an  applet and must be saved as a "SCREEN SHOT". If your data is not present in GenBank use this site.

CoreGenes  (D. Seto,  Bioinformatics & Computational Biology, George Mason Univ., U.S.A.) is designed to analyze two to five  genomes simultaneously, generating a table of related genes - orthologs and putative orthologs. These entries are linked  to their GenBank data.  It has a limit of 0.35 Mb, while the newer version CoreGenes 2.0 extends the limit to   approx. 2.0Mb. If your data is not present in GenBank use this site  The upgrade to this program is GenOrder 4.0 which will compare genomes up to 8Mb (Reference: Mahadevan P. &Seto D. 2010. BMC Research Notes 3:41).  
CoreGenes 3 (D. Seto & P. Mahadevan, Bioinformatics & Computational Biology, George Mason Univ., U.S.A) - tallies the total number of genes in common between the two genomes being compared; displays the percent value of genes in common with a specific genome; determines the unique genes contained in a pair of proteomes.  CoreGenes 3.5 is the batch CoreGenes server. I have tried this out on a group of P22likevirus species with great success.

PipeAlign (Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, France )  offers an integrated approach to protein family analysis through a cascade of five different sequence analysis programs  (BALLAST, DbClustal multiple alignment program, Rascal alignment analysis, removal of any sequences that do not  belong to the protein family are performed by the NorMD, and clustered into potential functional subfamilies using  Secator or DPC.  Reference: F. Plewniak et al. 2003. Nucleic Acids Research, 31: 3829-3832.


 JABAWS 2 - provides web services for multiple sequence alignment, prediction of protein disorder, and aminoacid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.0introduces protein disorder prediction services based on DisEMBL, IUPred, Ronn, GlobPlot and proteinsequence alignment conservation measures calculated by AACon. A new multiple sequence alignment service forClustal Omega is also provided, in addition to standard JABAWS:MSA services for Clustal W, MAFFT, MUSCLE,TCOFFEE and PROBCONS. JABA Web Services can be accessed from the Jalview desktop application and providemultiple alignment and sequence analysis calculations limited only by your own local computing resources. (Reference: Troshin, P.V. 2011. Bioinformatics. 27(14):2001-2002