ALIGNMENTS

COMPARE TWO SEQUENCES:

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

FFAS03: pairwise alignment  - nice presentation of results but server can be very slow. (Reference:  Jaroszewski et al. 2005. Nucl. Acids Res.  33: W284-W288)
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.

SIM  - Alignment tool for protein (ExPASy, Switzerland) gives fragmented alignments similar to LALIGN.  The results  can be visualized best with LALIGNVIEW.

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 (T.A. Tatusova & T. L. Madden. 1999. FEMS Microbiol Lett. 174:247-250 ) - 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: Finds the best local alignments between two sequences (EMBOSS) 
StretcherN (SRS EMBL-EBI) - finds the best global alignment between two sequences.
NeedleN (SRS EMBL-EBI) - Needleman-Wunsch global alignment between two sequences.

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. 

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).

COMPARE MULTIPLE SEQUENCES:

BACKGROUND INFORMATION: There are two good on-line help sites for CLUSTAL W. These are (a) On-line help for  CLUSTAL W, version 1.6, (Univ. Arizona, U.S.A.) and, (b) Multiple Alignment Resource Page, (VSNS, Virtual  School of Natural Sciences BioComputing Division (VSNS-BCD), Germany)

Several good sites: I prefer the EBI site since it offers the greatest flexibility in search strategy and output:

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).  Other sites offering ClustalW alignment are at the Pasteur Institute and  chEMBLnet.org
DbClustal - (Thompson et al. 2000. Nucleic Acid Research 28: 2919-2926; IGBMC, France) aligns sequences from a BlastP  database search with one query sequence. The alignment algorithm is based on ClustalW modified to incorporate  local alignment data in the form of anchor points between pairs of sequences. Very colorful output.

 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).

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). A similar type of output can be  obtained using SPEM (Laboratory of Biophysics & Bioinformatics, University of Buffalo, U.S.A.).  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).

Consensus (EMBL, Universitat Heidelberg) - takes CLUSTAL or MSF multiple alignments and calculates the consensus.
MultAlin - Multiple sequence alignment by Florence Corpet (Institut National de la Recherche Agronomique (INRA), France). N.B.  The results are presented in colour.

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.
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."
T-COFFEE (Swiss Institute for Bioinformatics) - reported to be more accurate than ClustalW for sequences with less  than 30% identity. Output in aln, GCG/MSF and phylip formats. This service can also be accessed here.

  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).

Alternative presentations of alignments:
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).
TeXshade (Pharmaceutical Institute University of Tübingen, Germany) - this program is available as as a stand-alone or online  at the Biology WorkBench and is alignment shading software completely written in TeX/LaTeX which can process  multiple sequence alignments in the .MSF and the .ALN file format. It provides in addition to common shading algorithms  special shading modes featuring functional aspects, e.g. charge or hydropathy, and a plenitude of commands for handling  shading colors, text styles, labels, legends and even allows the user to define completely new shading modes. TeXshade  combines highest flexibility and the habitual TeX output quality - with reasonable time expenditure. (Reference: Beitz, E.  (2000) Bioinformatics 16: 135-139).   
ESPript 2.2 - (IPBS, France) This requires that you save your alignment as a *.aln file. Good control over output  appearance and format is available (ps, tiff and gif).
CINEMA v5 - (University of Manchester, England) is a Colour INteractive Editor for Multiple Alignments for DNA and proteins.   Click on the Applet to start.
Multiple Align Show - (Bioinformatics.org/The Open Lab; University of Massachusetts Lowell) Allows considerable choice in  colouring alignments.
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.

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:

SCAN2 (Softberry.com) 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.

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). 

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.
YASS - perform DNA local alignments with results in dotplot and tabular form (Reference:  L.Noe & G. Kucherov.  2005. Nucl. Acids Res. 33: W540-W543).
  Dotlet - (Reference: T.Junier & M. Pagni. 2000. Bioinformatics 16:178-179)

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.

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.    
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
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.